Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008156.1 Hibiscus syriacus cultivar Beakdansim tig00110722_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 820393
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 5
Found at i:155728 original size:25 final size:26
Alignment explanation
Indices: 155692--155753 Score: 83
Period size: 25 Copynumber: 2.4 Consensus size: 26
155682 ATTTTTAATT
*
155692 TTTTACAAAATTACGAA-AATAGCACCA
1 TTTT-CAAAATTACCAATAA-AGCACCA
155719 TTTT-AAAATTACCAATAAAGCACCA
1 TTTTCAAAATTACCAATAAAGCACCA
155744 TTTTCAAAAT
1 TTTTCAAAAT
155754 ATTTACTAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
25 21 0.66
26 7 0.22
27 4 0.12
ACGTcount: A:0.47, C:0.18, G:0.05, T:0.31
Consensus pattern (26 bp):
TTTTCAAAATTACCAATAAAGCACCA
Found at i:155933 original size:18 final size:18
Alignment explanation
Indices: 155892--155934 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
155882 ACCCGGTCAA
**
155892 CAGTCAACGGGTCGGGTC
1 CAGTCAACGGGTCGGAAC
**
155910 GGGTCAACGGGTCGGAAC
1 CAGTCAACGGGTCGGAAC
155928 CAGTCAA
1 CAGTCAA
155935 ACCCTTTGAA
Statistics
Matches: 19, Mismatches: 6, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.23, C:0.26, G:0.37, T:0.14
Consensus pattern (18 bp):
CAGTCAACGGGTCGGAAC
Found at i:162924 original size:29 final size:30
Alignment explanation
Indices: 162892--162949 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 30
162882 TTTTTTTCAA
162892 AATTACAAAAATAGCACCA-TTTTAAAATT
1 AATTACAAAAATAGCACCATTTTTAAAATT
* *
162921 AATTACCAATATAGCACCATTTTTAAAAT
1 AATTACAAAAATAGCACCATTTTTAAAAT
162950 ACTTACTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 17 0.65
30 9 0.35
ACGTcount: A:0.48, C:0.16, G:0.03, T:0.33
Consensus pattern (30 bp):
AATTACAAAAATAGCACCATTTTTAAAATT
Found at i:164626 original size:14 final size:16
Alignment explanation
Indices: 164607--164640 Score: 54
Period size: 14 Copynumber: 2.2 Consensus size: 16
164597 GGGTCACTTG
164607 AAAAATTAA-A-AAGT
1 AAAAATTAACATAAGT
164621 AAAAATTAACATAAGT
1 AAAAATTAACATAAGT
164637 AAAA
1 AAAA
164641 TTGACTAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 9 0.50
15 1 0.06
16 8 0.44
ACGTcount: A:0.71, C:0.03, G:0.06, T:0.21
Consensus pattern (16 bp):
AAAAATTAACATAAGT
Found at i:171625 original size:164 final size:164
Alignment explanation
Indices: 171446--171759 Score: 515
Period size: 164 Copynumber: 1.9 Consensus size: 164
171436 ATTCAGTGAA
* *
171446 TATTTTATAATTTTTAATAATCGAATAACTTAATAAAATGATA-CTACATAATCATGAGATCATT
1 TATTTTATAATTTTTAATAATCAAATAACTTAATAAAATAATATC-ACATAATCATGAGATCATT
*
171510 TCATAAATTTTAATCATCATTATACTCAATAAAACAATAACTTATAATCCGA-ACTAATTGTGTA
65 TCATAAATTTTAATAATCATTATACTCAATAAAACAATAACTTATAAT-CGAGACTAATTGTGTA
*
171574 CTTTATTCAATATTCGTTTAATTTTTAATCAATTAT
129 CTTTACTCAATATTCGTTTAATTTTTAATCAATTAT
171610 TATTTTATAATTTTTAATAATCAAATAACTTAATAAAATAATATCACATAATCATGAGATCATTT
1 TATTTTATAATTTTTAATAATCAAATAACTTAATAAAATAATATCACATAATCATGAGATCATTT
* * * *
171675 CGTAATTTTTAATAATCATTATATTCAATAAAACAATAACTTATAATCTAGACTAATTGTGTACT
66 CATAAATTTTAATAATCATTATACTCAATAAAACAATAACTTATAATCGAGACTAATTGTGTACT
*
171740 TTACTCAATATTCTTTTAAT
131 TTACTCAATATTCGTTTAAT
171760 AATTCAATGT
Statistics
Matches: 139, Mismatches: 9, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
163 2 0.01
164 136 0.98
165 1 0.01
ACGTcount: A:0.41, C:0.12, G:0.04, T:0.42
Consensus pattern (164 bp):
TATTTTATAATTTTTAATAATCAAATAACTTAATAAAATAATATCACATAATCATGAGATCATTT
CATAAATTTTAATAATCATTATACTCAATAAAACAATAACTTATAATCGAGACTAATTGTGTACT
TTACTCAATATTCGTTTAATTTTTAATCAATTAT
Found at i:174690 original size:22 final size:22
Alignment explanation
Indices: 174665--174711 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
174655 TAAATTATTT
*
174665 AAATTATTTACGTTTATGTGTA
1 AAATGATTTACGTTTATGTGTA
174687 AAATGATTTACGTTTATGTGTA
1 AAATGATTTACGTTTATGTGTA
174709 AAA
1 AAA
174712 AATTTATTGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.36, C:0.04, G:0.15, T:0.45
Consensus pattern (22 bp):
AAATGATTTACGTTTATGTGTA
Found at i:176272 original size:659 final size:643
Alignment explanation
Indices: 174868--176077 Score: 1901
Period size: 659 Copynumber: 1.9 Consensus size: 643
174858 TGAGAAGATG
* * * *
174868 AAATCGGCATTGTTTTCGTATCAAATGATTATGTTAAAATATCATTCAAGATAAACAAAACTCTT
1 AAATC-GCATTGTTTTCGTATCAAATGATTATCTTAAAATAGCATGCAAGATAAACAAAACTCTC
*
174933 GAGGAGCTGATAACGAAGATTTCAAGGAAGGTTAATGTTGGAAGTAGTAGAAGAATGTCGTCGTT
65 GAGGAGATGATAACGAAGATTTCAAGGAAGGTTAATGTTGGAAGTAGTAGAAGAATGTCGTCGTT
174998 GTAGTACAAATTTCCAACATCATTGTTGCCATTAACTTATACAGCGTTCGAACTATCGAACAATG
130 GTAGTACAAATTTCCAACATCATTGTTGCCATTAACTTATACAGCGTTCGAAC-ATCGAACAATG
175063 ATGATGTTGAAATGATGTTGATTCTCAAAGTATTCAGACACCGATATTAGATGTATGCAAGTGTG
194 ATGATGTTGAAATGATGTTGATTCTCAAAGTATTCAGACACCGATATTAGATGTATGCAAGTGTG
175128 TCAGTGAGTGTTGTTCGGGGTTTGTCATTAAGCTCTCACTATGGGCTGGTTGAACAAGTTGATCA
259 TCAGTGAGTGTTGTTCGGGGTTTGTCATTAAGCTCTCACTATGGGCTGGTTGAACAAGTTGATCA
175193 AGTTGACAACCCGATTACAGTAATGTGTGATGATTTTAATGCCATAATGGGAAATCCGCATCATG
324 AGTTGACAACCCGATTACAGTAATGTGTGATGATTTTAATGCCATAATGGGAAATCCGCATCATG
175258 TTGTCGTTCAATTAACTTCAATGGGGAGACATTCATCAGAACTCCTTACGATCTGTACTGAGGTG
389 TTGTCGTTCAATTAACTTCAATGGGGAGACATTCATCAGAACTCCTTACGATCTGTACTGAGGTG
175323 GGTCCATGAACAATCTGTATGGCAACATCGAGACCAGTCTAGGGGCGTTTTTTTTGTGAAGCTCA
454 GGTCCATGAACAATCTGTATGGCAACATCGAGACCAGTCTAGGGGCG-TTTTTTTGTGAAGCTCA
* * * *
175388 AGGGACAAGCTCAAACTTGGATCAAGGCGGTTTCAATTGTTTTTTTTGTAGACATAATATTGTTG
518 AGGGACAAGCTCAAACTTGGATCAAGGCGG-TTCAATTG--TTCTATGCAGACATAATATAGTTG
* * * * * * * * * *
175453 CACTTTCAAACTCTAATAATGGCGCGAATTTCAACTATTATTTATTATGATGGAGAAATTTGAGA
580 CAATCTCAAA--CAAAAAATGGCGCGAA-TTCAAC-ATGA--TATTATGATGAACAAACTTCACA
**
175518 AGATG
639 AGAAC
* * * * *
175523 AAATCGGCGTTGTTTTCGTATCAAATGATTATGTTAAAATATCATTCAAGATAAACAAAACTCTT
1 AAATC-GCATTGTTTTCGTATCAAATGATTATCTTAAAATAGCATGCAAGATAAACAAAACTCTC
*
175588 GAGGAGCTGATAACGAAGATTTCAAGGAAGGTTAATGTTGGAAGTAGTAGAAGAATGTCGTCGTT
65 GAGGAGATGATAACGAAGATTTCAAGGAAGGTTAATGTTGGAAGTAGTAGAAGAATGTCGTCGTT
175653 GTAGTACAAATTTCCAACATCATTGTTGCCATTAAC-TATACA-CGTTCG-A-ATCGAACAATGA
130 GTAGTACAAATTTCCAACATCATTGTTGCCATTAACTTATACAGCGTTCGAACATCGAACAATGA
175714 TGA-GTTGAAATGATTGGTTGATTCTCAAAGTAATTATTCAGACACCGATATTGAGATGTATGCA
195 TGATGTTGAAATGA-T-GTTGATTCTCAAAG----TATTCAGACACCGATATT-AGATGTATGC-
*
175778 AAGTTTGTTCAAGTGAGTGTTGTTCGGGGTTTGTCATTAAGCTCTCACTATGGGCTGGTTGAACA
252 AAGTGTG-TC-AGTGAGTGTTGTTCGGGGTTTGTCATTAAGCTCTCACTATGGGCTGGTTGAACA
175843 AGTTGATCAAGTTGACAACCCGATTACAGTAATGTGTGATGATTTTAATGCCATAATGGGAAATC
315 AGTTGATCAAGTTGACAACCCGATTACAGTAATGTGTGATGATTTTAATGCCATAATGGGAAATC
175908 CGCATCATGTTGTCGTTCAATTAACTTCAATGGGGAGACATTCATCAGAACTCCTTACGATCTGT
380 CGCATCATGTTGTCGTTCAATTAACTTCAATGGGGAGACATTCATCAGAACTCCTTACGATCTGT
175973 ACTGAGGTGGGTCCATGAACAATCTGTATGGCAACATCGAGACCAGTTCTAGGGGCG-TTTTTTG
445 ACTGAGGTGGGTCCATGAACAATCTGTATGGCAACATCGAGACCAG-TCTAGGGGCGTTTTTTTG
176037 TGAAGCTCAAGGGACAAGCTCAAACTTGGATGCAAGGCGGT
509 TGAAGCTCAAGGGACAAGCTCAAACTTGGAT-CAAGGCGGT
176078 CATGTCTATC
Statistics
Matches: 541, Mismatches: 2, Indels: 21
0.96 0.00 0.04
Matches are distributed among these distances:
649 10 0.02
650 16 0.03
651 14 0.03
652 1 0.00
653 6 0.01
654 6 0.01
655 183 0.34
656 10 0.02
657 6 0.01
658 41 0.08
659 238 0.44
660 10 0.02
ACGTcount: A:0.31, C:0.15, G:0.22, T:0.32
Consensus pattern (643 bp):
AAATCGCATTGTTTTCGTATCAAATGATTATCTTAAAATAGCATGCAAGATAAACAAAACTCTCG
AGGAGATGATAACGAAGATTTCAAGGAAGGTTAATGTTGGAAGTAGTAGAAGAATGTCGTCGTTG
TAGTACAAATTTCCAACATCATTGTTGCCATTAACTTATACAGCGTTCGAACATCGAACAATGAT
GATGTTGAAATGATGTTGATTCTCAAAGTATTCAGACACCGATATTAGATGTATGCAAGTGTGTC
AGTGAGTGTTGTTCGGGGTTTGTCATTAAGCTCTCACTATGGGCTGGTTGAACAAGTTGATCAAG
TTGACAACCCGATTACAGTAATGTGTGATGATTTTAATGCCATAATGGGAAATCCGCATCATGTT
GTCGTTCAATTAACTTCAATGGGGAGACATTCATCAGAACTCCTTACGATCTGTACTGAGGTGGG
TCCATGAACAATCTGTATGGCAACATCGAGACCAGTCTAGGGGCGTTTTTTTGTGAAGCTCAAGG
GACAAGCTCAAACTTGGATCAAGGCGGTTCAATTGTTCTATGCAGACATAATATAGTTGCAATCT
CAAACAAAAAATGGCGCGAATTCAACATGATATTATGATGAACAAACTTCACAAGAAC
Found at i:176944 original size:38 final size:36
Alignment explanation
Indices: 176877--176947 Score: 92
Period size: 38 Copynumber: 1.9 Consensus size: 36
176867 CTGAATACAA
176877 CAAACTTACAATAAGTATTAAATTGTAAATAATAAT
1 CAAACTTACAATAAGTATTAAATTGTAAATAATAAT
176913 CAAA-TTACAATAACTGATATTAAA-TGATAAATAAT
1 CAAACTTACAATAA--G-TATTAAATTG-TAAATAAT
176948 TTAACTGATA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
35 9 0.29
36 4 0.13
37 3 0.10
38 15 0.48
ACGTcount: A:0.54, C:0.08, G:0.06, T:0.32
Consensus pattern (36 bp):
CAAACTTACAATAAGTATTAAATTGTAAATAATAAT
Found at i:177407 original size:30 final size:30
Alignment explanation
Indices: 177373--177448 Score: 122
Period size: 27 Copynumber: 2.6 Consensus size: 30
177363 AAACCAGGTG
*
177373 AAGGCGGCGGCGGCATCATCTGGTAAGGGA
1 AAGGCGGTGGCGGCATCATCTGGTAAGGGA
177403 AAGGCGGTGGCGG---CATCTGGTAAGGGA
1 AAGGCGGTGGCGGCATCATCTGGTAAGGGA
177430 AAGGCGGTGGCGGCATCAT
1 AAGGCGGTGGCGGCATCAT
177449 ATATAGTTGA
Statistics
Matches: 42, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
27 27 0.64
30 15 0.36
ACGTcount: A:0.22, C:0.18, G:0.45, T:0.14
Consensus pattern (30 bp):
AAGGCGGTGGCGGCATCATCTGGTAAGGGA
Found at i:180521 original size:21 final size:22
Alignment explanation
Indices: 180467--180523 Score: 64
Period size: 25 Copynumber: 2.5 Consensus size: 22
180457 GTTCCGTTTA
180467 AGTGT-AAACTAATTTATTGGAGG
1 AGTGTAAAACTAATTTATT-G-GG
*
180490 AGAGTACAAACTAATTTATT-GG
1 AGTGTA-AAACTAATTTATTGGG
180512 AGTGTAAAACTA
1 AGTGTAAAACTA
180524 CACATTTAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
21 6 0.20
22 7 0.23
23 4 0.13
25 13 0.43
ACGTcount: A:0.40, C:0.07, G:0.21, T:0.32
Consensus pattern (22 bp):
AGTGTAAAACTAATTTATTGGG
Found at i:185319 original size:15 final size:16
Alignment explanation
Indices: 185299--185328 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
185289 ACTTTGACCC
185299 GAAAAGTCA-ATTTTT
1 GAAAAGTCATATTTTT
185314 GAAAAGTCATATTTT
1 GAAAAGTCATATTTT
185329 ATATTTTTCG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.40, C:0.07, G:0.13, T:0.40
Consensus pattern (16 bp):
GAAAAGTCATATTTTT
Found at i:186620 original size:3 final size:3
Alignment explanation
Indices: 186612--186664 Score: 54
Period size: 3 Copynumber: 17.0 Consensus size: 3
186602 CGGGTCTTTT
* *
186612 TTA TTA TTA TTTA TAA ATA TTTA TTA TTA TTA TTA TT- TATA TTA TTA
1 TTA TTA TTA -TTA TTA TTA -TTA TTA TTA TTA TTA TTA T-TA TTA TTA
186659 TTA TTA
1 TTA TTA
186665 ATATATAAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
2 1 0.02
3 35 0.83
4 6 0.14
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:192413 original size:26 final size:25
Alignment explanation
Indices: 192384--192455 Score: 65
Period size: 26 Copynumber: 2.7 Consensus size: 25
192374 AAACAAACAT
*
192384 AATAGAAGCAAAGAAAAAAATAGAAA
1 AATAGAA-CAAAGAAAAAAAGAGAAA
192410 AATAGAA-AAAGAATAAAGAAGAGAAAA
1 AATAGAACAAAGAA-AAA-AAGAG-AAA
* *
192437 GAAAAAAACAAAGAAAAAA
1 -AATAGAACAAAGAAAAAA
192456 GCAAAGAGAA
Statistics
Matches: 38, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
24 6 0.16
25 3 0.08
26 11 0.29
27 4 0.11
28 8 0.21
29 6 0.16
ACGTcount: A:0.76, C:0.03, G:0.15, T:0.06
Consensus pattern (25 bp):
AATAGAACAAAGAAAAAAAGAGAAA
Found at i:192440 original size:31 final size:30
Alignment explanation
Indices: 192393--192471 Score: 83
Period size: 31 Copynumber: 2.6 Consensus size: 30
192383 TAATAGAAGC
*
192393 AAAGAAA-A-AAATAGAAAAATAGAAAAAGAAT
1 AAAGAAAGAGAAA-AGAAAAA-A-AAAAAGAAA
*
192424 AAAG-AAGAGAAAAGAAAAAAACAAAGAAA
1 AAAGAAAGAGAAAAGAAAAAAAAAAAGAAA
192453 AAAGCAAAGAGAAAAGAAA
1 AAAG-AAAGAGAAAAGAAA
192472 CAAAGGAAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
29 11 0.26
30 3 0.07
31 25 0.60
32 3 0.07
ACGTcount: A:0.77, C:0.03, G:0.16, T:0.04
Consensus pattern (30 bp):
AAAGAAAGAGAAAAGAAAAAAAAAAAGAAA
Found at i:192465 original size:14 final size:14
Alignment explanation
Indices: 192436--192517 Score: 53
Period size: 14 Copynumber: 5.6 Consensus size: 14
192426 AGAAGAGAAA
*
192436 AGAAAAAAAC-AA-
1 AGAAAAAAGCAAAG
192448 AGAAAAAAGCAAAG
1 AGAAAAAAGCAAAG
*
192462 AGAAAAGAAACAAAG
1 AGAAAA-AAGCAAAG
*
192477 -GAAAAAAATCAAAG
1 AG-AAAAAAGCAAAG
192491 CAAAAGAAAAAAGCAAAG
1 ----AGAAAAAAGCAAAG
*
192509 AGCAAAAAG
1 AGAAAAAAG
192518 AAAACAAGGA
Statistics
Matches: 56, Mismatches: 5, Indels: 16
0.73 0.06 0.21
Matches are distributed among these distances:
12 9 0.16
13 2 0.04
14 22 0.39
15 11 0.20
18 11 0.20
19 1 0.02
ACGTcount: A:0.73, C:0.09, G:0.17, T:0.01
Consensus pattern (14 bp):
AGAAAAAAGCAAAG
Found at i:192504 original size:13 final size:14
Alignment explanation
Indices: 192434--192507 Score: 61
Period size: 14 Copynumber: 5.6 Consensus size: 14
192424 AAAGAAGAGA
192434 AAAG-AAAA-AAAC
1 AAAGCAAAAGAAAC
*
192446 AAAG-AAAA-AAGC
1 AAAGCAAAAGAAAC
*
192458 AAAGAGAAAAGAAAC
1 AAAG-CAAAAGAAAC
*
192473 AAAGGAAAA-AAATC
1 AAAGCAAAAGAAA-C
192487 AAAGCAAAAGAAA-
1 AAAGCAAAAGAAAC
192500 AAAGCAAA
1 AAAGCAAA
192508 GAGCAAAAAG
Statistics
Matches: 54, Mismatches: 3, Indels: 9
0.82 0.05 0.14
Matches are distributed among these distances:
12 15 0.28
13 11 0.20
14 18 0.33
15 10 0.19
ACGTcount: A:0.76, C:0.08, G:0.15, T:0.01
Consensus pattern (14 bp):
AAAGCAAAAGAAAC
Found at i:192509 original size:12 final size:12
Alignment explanation
Indices: 192434--192468 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
192424 AAAGAAGAGA
*
192434 AAAGAAAAAAAC
1 AAAGAAAAAAGC
192446 AAAGAAAAAAGC
1 AAAGAAAAAAGC
*
192458 AAAGAGAAAAG
1 AAAGAAAAAAG
192469 AAACAAAGGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.77, C:0.06, G:0.17, T:0.00
Consensus pattern (12 bp):
AAAGAAAAAAGC
Found at i:192521 original size:40 final size:38
Alignment explanation
Indices: 192415--192521 Score: 94
Period size: 40 Copynumber: 2.8 Consensus size: 38
192405 AGAAAAATAG
* *
192415 AAAAAGAATAAAG--AAGAGAAAAGAAAAAAACAAAGA
1 AAAAAGAAAAAAGAAAAGAAAAAAGAAAAAAACAAAGA
* *
192451 AAAAAGCAAAGAGAAAAGAAACAAAGGAAAAAAATCAAAG-
1 AAAAAGAAAAAAGAAAAGAAA-AAA-GAAAAAAA-CAAAGA
* *
192491 CAAAAGAAAAAAGCAAAGAGCAAAAAGAAAA
1 AAAAAGAAAAAAG-AAA-AGAAAAAAGAAAA
192522 CAAGGAGCAT
Statistics
Matches: 56, Mismatches: 8, Indels: 10
0.76 0.11 0.14
Matches are distributed among these distances:
36 10 0.18
38 5 0.09
39 3 0.05
40 23 0.41
41 11 0.20
42 4 0.07
ACGTcount: A:0.75, C:0.07, G:0.17, T:0.02
Consensus pattern (38 bp):
AAAAAGAAAAAAGAAAAGAAAAAAGAAAAAAACAAAGA
Found at i:194376 original size:105 final size:103
Alignment explanation
Indices: 194216--194443 Score: 275
Period size: 105 Copynumber: 2.2 Consensus size: 103
194206 CAAACTTCGC
194216 CTCGCTTGAGACATTTTCTTTGAGATACAAATTTCGAATTTGATTCACTTGAAACAAAAATTAAT
1 CTCGCTTGAGACATTTTCTTTGAGATACAAATTTCGAATTTGATTCACTTGAAACAAAAA-TAAT
*
194281 CTCACTTGAGATTGTTATTTCTTT-AAAAA-AAA-TTAT
65 CTCACTTGAGATCGTTATTTCTTTCAAAAACAAACTTAT
* * * *
194317 CTCGTTTGAGACATTTTTTCCTTTGAGAATACAAATTTCGATTTTGTTTCACATT-AAACAAAGA
1 CTCGCTTGAGACA--TTTT-CTTTGAG-ATACAAATTTCGAATTTGATTCAC-TTGAAACAAAAA
* * * *
194381 TGATCTCACTTGAGATCGTTTTTTTTTTCAAAAACAAACTTTGT
61 TAATCTCACTTGAGATCGTTATTTCTTTCAAAAACAAAC-TTAT
*
194425 CTCGCTTGAGACAATTTCT
1 CTCGCTTGAGACATTTTCT
194444 CTAAAAACAA
Statistics
Matches: 107, Mismatches: 11, Indels: 14
0.81 0.08 0.11
Matches are distributed among these distances:
101 12 0.11
103 4 0.04
104 31 0.29
105 37 0.35
106 8 0.07
108 15 0.14
ACGTcount: A:0.32, C:0.16, G:0.12, T:0.41
Consensus pattern (103 bp):
CTCGCTTGAGACATTTTCTTTGAGATACAAATTTCGAATTTGATTCACTTGAAACAAAAATAATC
TCACTTGAGATCGTTATTTCTTTCAAAAACAAACTTAT
Found at i:194460 original size:36 final size:36
Alignment explanation
Indices: 194410--194513 Score: 172
Period size: 36 Copynumber: 2.9 Consensus size: 36
194400 TTTTTTTTTC
* *
194410 AAAAACAAACTTTGTCTCGCTTGAGACAATTTCTCT
1 AAAAACAAATTTTGTCTCGTTTGAGACAATTTCTCT
194446 AAAAACAAATTTTGTCTCGTTTGAGACAATTTCTCT
1 AAAAACAAATTTTGTCTCGTTTGAGACAATTTCTCT
* *
194482 AAAAACAAATATTGTCTCATTTGAGACAATTT
1 AAAAACAAATTTTGTCTCGTTTGAGACAATTT
194514 TCCAAGTTAT
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 64 1.00
ACGTcount: A:0.37, C:0.17, G:0.11, T:0.36
Consensus pattern (36 bp):
AAAAACAAATTTTGTCTCGTTTGAGACAATTTCTCT
Found at i:194814 original size:132 final size:131
Alignment explanation
Indices: 194590--194834 Score: 309
Period size: 132 Copynumber: 1.9 Consensus size: 131
194580 GATCTTTAAG
* **
194590 TCTGTTTCACTTGAAATAAAAAAAATCTTTGAGTATGTTTCTTTGATAACAAAATTTTGTCTATT
1 TCTGTTTCACTTGAAACAAAAAAAATCTTTGAGTATGTTTCTTTGATAACAAAATTTTGTCTAGC
**
194655 TTGAGAAGGTTTCTTTTGAAAAATCTTTGAGT-ATGTTTCTTTGGAAACAACATTTACCATCTGT
66 TTGAGAAGGTTTCTCGTGAAAAATCTTTGAGTCA--TTTCTTTGGAAACAACATTTACCATCTGT
194719 GAT
129 GAT
* *** * *
194722 TCTGTTTCCCTTGAAACAAAACTCATCTTTGAGTATTTTTCTTTTGA-AACAAAATTTTGTCTCG
1 TCTGTTTCACTTGAAACAAAAAAAATCTTTGAGTATGTTTC-TTTGATAACAAAATTTTGTCTAG
*
194786 CTTGAGACA-GTTT-TCGTGAAAAAGTCTTTGAGTCATTTCTTTTGAAACA
65 CTTGAGA-AGGTTTCTCGTGAAAAA-TCTTTGAGTCATTTCTTTGGAAACA
194835 TCCATCTTTG
Statistics
Matches: 97, Mismatches: 12, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
131 21 0.22
132 69 0.71
133 7 0.07
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.42
Consensus pattern (131 bp):
TCTGTTTCACTTGAAACAAAAAAAATCTTTGAGTATGTTTCTTTGATAACAAAATTTTGTCTAGC
TTGAGAAGGTTTCTCGTGAAAAATCTTTGAGTCATTTCTTTGGAAACAACATTTACCATCTGTGA
T
Found at i:195148 original size:64 final size:61
Alignment explanation
Indices: 195027--195159 Score: 151
Period size: 64 Copynumber: 2.1 Consensus size: 61
195017 ATTTTCTGAA
* * *
195027 AAACAAAATTTTGTCTCTCATGGCAATGTCTTTTGAAAAATCATTGAATATGTTTCTTTGG
1 AAACAAAATTTTGTCTCTCATGACAATGTCTTTAGAAAAATCATTGAATATGTTTCTTTAG
* * * * *
195088 AAACAAAATTTTGTTTCTCTCGA-GACAATTTCTTTGAGAAAAATCTTTGAGTTTTTTTCTTTAG
1 AAACAAAATTTTG--TCTCTC-ATGACAATGTCTTT-AGAAAAATCATTGAATATGTTTCTTTAG
195152 AAACAAAA
1 AAACAAAA
195160 ATTTACCATC
Statistics
Matches: 60, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
61 13 0.22
63 16 0.27
64 31 0.52
ACGTcount: A:0.34, C:0.13, G:0.13, T:0.41
Consensus pattern (61 bp):
AAACAAAATTTTGTCTCTCATGACAATGTCTTTAGAAAAATCATTGAATATGTTTCTTTAG
Found at i:195192 original size:37 final size:36
Alignment explanation
Indices: 195151--195230 Score: 101
Period size: 35 Copynumber: 2.2 Consensus size: 36
195141 TTTTTCTTTA
* *
195151 GAAACAAAAATTTACCATCTTTGAGTAT-GTTTCCCTT
1 GAAACAAAAA-CTAACATCTTTGAG-ATCGTTTCCCTT
*
195188 GAAAC-AAAACTAACATCTTTGAGATCGTTTCTCTT
1 GAAACAAAAACTAACATCTTTGAGATCGTTTCCCTT
195223 GAAACAAA
1 GAAACAAA
195231 TTTTGTCTCA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
34 2 0.05
35 25 0.66
36 6 0.16
37 5 0.13
ACGTcount: A:0.38, C:0.19, G:0.11, T:0.33
Consensus pattern (36 bp):
GAAACAAAAACTAACATCTTTGAGATCGTTTCCCTT
Found at i:195430 original size:28 final size:28
Alignment explanation
Indices: 195385--195453 Score: 95
Period size: 28 Copynumber: 2.4 Consensus size: 28
195375 AGACAATGTA
195385 TTTTGAAACACATCATCTTTGAGTTTGTTT-
1 TTTTGAAACA-A--ATCTTTGAGTTTGTTTC
195415 TTCTTGAAACAAATCTTTGAGTTTGTTTC
1 TT-TTGAAACAAATCTTTGAGTTTGTTTC
195444 TTTTGAAACA
1 TTTTGAAACA
195454 TCACCTTTGT
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
28 24 0.65
29 2 0.05
30 3 0.08
31 8 0.22
ACGTcount: A:0.26, C:0.13, G:0.13, T:0.48
Consensus pattern (28 bp):
TTTTGAAACAAATCTTTGAGTTTGTTTC
Found at i:195827 original size:135 final size:133
Alignment explanation
Indices: 195546--195846 Score: 415
Period size: 135 Copynumber: 2.3 Consensus size: 133
195536 CTGACCAGAC
* *
195546 CTCCTCATCACGTAGGAGCCGTGTCAACCTT-GATAACCAGCCGTCCTCATCGCGTAGGAACCGA
1 CTCCTCATCACGTAGGAGCCGTGTCACCCTTAGATAACCAGCCGTCCTCATCACGTAGGAACCGA
* * *
195610 GTTATCACCTTCCTAAAGATGACTAGAACTCTTCATCACGTATGAACCGTGTCATCCCCCAACTA
66 GTTATCACCTTCCTAAAGATGACAAGAACTCTTCAACACGTATGAACCGTGTCATCCCCCAACCA
*
195675 GAT
131 AAT
* * *
195678 CTCCTCATCGCGTAGGAGTCGTGTCACCCTTAGATAACCAGTCGTCCTCATCACGTAGGAACCGA
1 CTCCTCATCACGTAGGAGCCGTGTCACCCTTAGATAACCAGCCGTCCTCATCACGTAGGAACCGA
* *** * *
195743 GTTATCACCCTTCCTAAAGATGGCCAAGAACTCTTCAACACGTATGAGTTGTGTCATCCCTCGAC
66 GTTATCA-CCTTCCTAAAGAT-GACAAGAACTCTTCAACACGTATGAACCGTGTCATCCCCCAAC
195808 CAAAT
129 CAAAT
* * *
195813 TTCCTCATCACGTAGGAACCATGTCACCCTTAGA
1 CTCCTCATCACGTAGGAGCCGTGTCACCCTTAGA
195847 CGACCCGAAC
Statistics
Matches: 146, Mismatches: 20, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
132 28 0.19
133 38 0.26
134 13 0.09
135 67 0.46
ACGTcount: A:0.26, C:0.31, G:0.18, T:0.25
Consensus pattern (133 bp):
CTCCTCATCACGTAGGAGCCGTGTCACCCTTAGATAACCAGCCGTCCTCATCACGTAGGAACCGA
GTTATCACCTTCCTAAAGATGACAAGAACTCTTCAACACGTATGAACCGTGTCATCCCCCAACCA
AAT
Found at i:196039 original size:3 final size:3
Alignment explanation
Indices: 196031--196089 Score: 66
Period size: 3 Copynumber: 19.0 Consensus size: 3
196021 CGGGTCTTTT
* *
196031 TTA TTA TTA TTTA TAA ATA TTTA TTA TTA TTA TTA TTA TTA TT- TATA
1 TTA TTA TTA -TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA T-TA
196078 TTA TTA TTA TTA
1 TTA TTA TTA TTA
196090 ATATATAAAT
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
2 1 0.02
3 41 0.85
4 6 0.12
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:197740 original size:30 final size:30
Alignment explanation
Indices: 197706--197762 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
197696 CTATTTTATT
*
197706 TATTTTAGACC-CTTAAGTTTCTGTTTTTAC
1 TATTTTAG-CCACTTAAGTTTATGTTTTTAC
*
197736 TATTTTAGCCATTTAAGTTTATGTTTT
1 TATTTTAGCCACTTAAGTTTATGTTTT
197763 GGCCATATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 2 0.08
30 22 0.92
ACGTcount: A:0.21, C:0.12, G:0.11, T:0.56
Consensus pattern (30 bp):
TATTTTAGCCACTTAAGTTTATGTTTTTAC
Found at i:201363 original size:346 final size:344
Alignment explanation
Indices: 200725--201590 Score: 1162
Period size: 346 Copynumber: 2.5 Consensus size: 344
200715 TGAAATGGGT
* * *
200725 CATTATTGCTGCAATAAATAACCTTTGAAAAGTAGCTGACACAATACATTAATTGAGCACTGGAA
1 CATTATTGCTGCAATAAATAACCTCTAAAAAGTAGCTGACACGATACATTAATTGAGCACT-GAA
* *
200790 AGTAGCTGAAACAGTGAATAATTTGGTCTGGTTGAAATACATGTTTTTATTATTTGAAGTGATAA
65 AGTAGCTGAAACAGTGAATAATTTGGCCTGGTTGAAATACATGTTTTTA-TAATTGAAGTGATAA
* ** * * *
200855 TTCAACACT-ATAAAGTTTTCTGATTTGAGTTTGCATTTCGTTAAACAATAGCTGGAATGGTGCA
129 TTCAACACTGA-AAAGTTTTCTGATTTGAGTTTGTATTTCACTGAACAATACCTGGAAGGGTGCA
* * ** **
200919 TTATTTTTCCTGAGTTAAAAACATATTTTCTGATTTAAGTTGATATATCACTGAAAAGTTGTTGG
193 TTATTTTGCCTGAGTTAAAAACACATTTTCTGATTTAAGTTGATATATCACTGAAAAGTTACTAA
* * *** * **
200984 AGATGATAATACACCGCTATTTCACTCGTTTTCTAAAAAGTTTCTTGTATTTTGTAGTAAATGAC
258 AGATGATAATACACCACTATTTCACTCGTTTTCTAAAAAGTTACTCCAATTCTACAGTAAATGAC
*
201049 CAACAAAATAAACCAACCATTG
323 CAACAAAATAAACCAAACATTG
* * * * *
201071 CATTATTGCTGCAATAAATGACCTCTAAAAAGTAGTTGTCACGGTGCATTAATTGAGCACTGCAA
1 CATTATTGCTGCAATAAATAACCTCTAAAAAGTAGCTGACACGATACATTAATTGAGCACTG-AA
** * * *
201136 AGTAGCTGAAACAACGAATAATTTGGCCTGGTTGAAATACATATTTTTATGATGTGAAGTGATGA
65 AGTAGCTGAAACAGTGAATAATTTGGCCTGGTTGAAATACATGTTTTTATAAT-TGAAGTGATAA
* * *
201201 TTCAACACTGAAAAATTTGCTAATTTGAGTTTGTATTTCACTGAACAATACCTGGAAGGGTGCAT
129 TTCAACACTGAAAAGTTTTCTGATTTGAGTTTGTATTTCACTGAACAATACCTGGAAGGGTGCAT
*
201266 TATTTTGCCTGAGTTAAAAACACATTTTCTGATTTGAGTTGATATATCACTGAAAAGTTACTAAA
194 TATTTTGCCTGAGTTAAAAACACATTTTCTGATTTAAGTTGATATATCACTGAAAAGTTACTAAA
* *
201331 GATGATAATGCACCACTATTTCACAT-GTTTTCTGAAAAGTTACTCCAATTCTACAGTAAATGAC
259 GATGATAATACACCACTATTTCAC-TCGTTTTCTAAAAAGTTACTCCAATTCTACAGTAAATGAC
**
201395 CAACAAAATAAACCAAATGTTG
323 CAACAAAATAAACCAAACATTG
* ** * *
201417 TATTATTGCTAAAATAAATTACCTCTAAAAAGTAGCTGACACGATACATTAATTGAGCATTAGAA
1 CATTATTGCTGCAATAAATAACCTCTAAAAAGTAGCTGACACGATACATTAATTGAGCACT-GAA
*
201482 AGTAGCTGAAACAGTGAATAATTTGGCCTGGTTGACATACATGTTTTTATTAATTGAAGTGA-AA
65 AGTAGCTGAAACAGTGAATAATTTGGCCTGGTTGAAATACATGTTTTTA-TAATTGAAGTGATAA
* * *
201546 ATCAACATTGAAAAGTTTTCTGATTTAAGTTTGTATTTCACTGAA
129 TTCAACACTGAAAAGTTTTCTGATTTGAGTTTGTATTTCACTGAA
201591 AAGTTACTGA
Statistics
Matches: 449, Mismatches: 65, Indels: 13
0.85 0.12 0.02
Matches are distributed among these distances:
345 43 0.10
346 400 0.89
347 6 0.01
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.34
Consensus pattern (344 bp):
CATTATTGCTGCAATAAATAACCTCTAAAAAGTAGCTGACACGATACATTAATTGAGCACTGAAA
GTAGCTGAAACAGTGAATAATTTGGCCTGGTTGAAATACATGTTTTTATAATTGAAGTGATAATT
CAACACTGAAAAGTTTTCTGATTTGAGTTTGTATTTCACTGAACAATACCTGGAAGGGTGCATTA
TTTTGCCTGAGTTAAAAACACATTTTCTGATTTAAGTTGATATATCACTGAAAAGTTACTAAAGA
TGATAATACACCACTATTTCACTCGTTTTCTAAAAAGTTACTCCAATTCTACAGTAAATGACCAA
CAAAATAAACCAAACATTG
Found at i:205075 original size:20 final size:20
Alignment explanation
Indices: 205046--205083 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
205036 TTTCAAAGAG
205046 ATGCACCGATGCACCAATCC
1 ATGCACCGATGCACCAATCC
*
205066 ATGCATCGATGCACCAAT
1 ATGCACCGATGCACCAAT
205084 TAATTTTTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.34, G:0.16, T:0.18
Consensus pattern (20 bp):
ATGCACCGATGCACCAATCC
Found at i:205152 original size:45 final size:46
Alignment explanation
Indices: 205103--205193 Score: 139
Period size: 45 Copynumber: 2.0 Consensus size: 46
205093 AAACATCAAA
* * *
205103 TGCATTTTATGCATCGATGCAC-ATACCATGAATTGATGCACTCAG
1 TGCATTTGATGCATCGATGCACAAGACCATGAATCGATGCACTCAG
*
205148 TGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACTCAG
1 TGCATTTGATGCATCGATGCACAAGACCATGAATCGATGCACTCAG
205194 GCTTTTTCAA
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
45 21 0.51
46 20 0.49
ACGTcount: A:0.29, C:0.24, G:0.20, T:0.27
Consensus pattern (46 bp):
TGCATTTGATGCATCGATGCACAAGACCATGAATCGATGCACTCAG
Found at i:213814 original size:20 final size:20
Alignment explanation
Indices: 213785--213822 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
213775 TTTCAAAGAG
213785 ATGCACCGATGCACCAATCC
1 ATGCACCGATGCACCAATCC
*
213805 ATGCATCGATGCACCAAT
1 ATGCACCGATGCACCAAT
213823 TAATTTTTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.34, G:0.16, T:0.18
Consensus pattern (20 bp):
ATGCACCGATGCACCAATCC
Found at i:219026 original size:82 final size:82
Alignment explanation
Indices: 218873--219072 Score: 265
Period size: 82 Copynumber: 2.4 Consensus size: 82
218863 AATAAAAAAG
* * * * * *
218873 CTTAAGCAAGGTGGAGTCTGCAGTAGGGGGAGTGTTGGTGCATGGTTTTGCATACACTTTGTTTT
1 CTTAAACAAGGTGGAGTCTGCAGTAGGGGGAGTGTTGATGCATGGTGTTGCATACACCTCGGTTT
218938 CACGTGAAGTTGGTGTT
66 CACGTGAAGTTGGTGTT
* * **
218955 CTTAAACAAGGTGGAGTCTACAGTAGGGGGAGTGTTGATGCATGGTGTTGTATGTACCTCGGTTT
1 CTTAAACAAGGTGGAGTCTGCAGTAGGGGGAGTGTTGATGCATGGTGTTGCATACACCTCGGTTT
*
219020 CGCGTGAAGTTGGTGTT
66 CACGTGAAGTTGGTGTT
* * * *
219037 CTTAAACAAGGAGGTGTTTGCAGTAGGGGGAATGTT
1 CTTAAACAAGGTGGAGTCTGCAGTAGGGGGAGTGTT
219073 AGTGTATATG
Statistics
Matches: 102, Mismatches: 16, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
82 102 1.00
ACGTcount: A:0.20, C:0.12, G:0.35, T:0.33
Consensus pattern (82 bp):
CTTAAACAAGGTGGAGTCTGCAGTAGGGGGAGTGTTGATGCATGGTGTTGCATACACCTCGGTTT
CACGTGAAGTTGGTGTT
Found at i:220299 original size:28 final size:30
Alignment explanation
Indices: 220267--220326 Score: 79
Period size: 28 Copynumber: 2.1 Consensus size: 30
220257 TTAAAAAATC
* * *
220267 TTAAATTATACAAA-TAACATA-ATATAAT
1 TTAAATAAAACAAATTAAAATATATATAAT
220295 TTAAATAAAACAAATTAAAATATATATAAT
1 TTAAATAAAACAAATTAAAATATATATAAT
220325 TT
1 TT
220327 TGATTGAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 12 0.44
29 6 0.22
30 9 0.33
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (30 bp):
TTAAATAAAACAAATTAAAATATATATAAT
Found at i:224656 original size:2 final size:2
Alignment explanation
Indices: 224651--224677 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
224641 TTTCATACAT
224651 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC A
224678 TACATATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:229232 original size:72 final size:72
Alignment explanation
Indices: 229111--229258 Score: 289
Period size: 72 Copynumber: 2.1 Consensus size: 72
229101 CACAGTCAAA
229111 ATCC-TTGATGTTATCGGATATGGTTGAAAAGTCATTTGCCACTGTTGTTGCAGTGCTTTTCAAT
1 ATCCGTTGATGTTATCGGATATGGTTGAAAAGTCATTTGCCACTGTTGTTGCAGTGCTTTTCAAT
229175 CCCTGTT
66 CCCTGTT
229182 ATCCGTTGATGTTATCGGATATGGTTGAAAAGTCATTTGCCACTGTTGTTGCAGTGCTTTTCAAT
1 ATCCGTTGATGTTATCGGATATGGTTGAAAAGTCATTTGCCACTGTTGTTGCAGTGCTTTTCAAT
229247 CCCTGTT
66 CCCTGTT
229254 ATCCG
1 ATCCG
229259 AGAATTATTT
Statistics
Matches: 76, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
71 4 0.05
72 72 0.95
ACGTcount: A:0.20, C:0.19, G:0.22, T:0.40
Consensus pattern (72 bp):
ATCCGTTGATGTTATCGGATATGGTTGAAAAGTCATTTGCCACTGTTGTTGCAGTGCTTTTCAAT
CCCTGTT
Found at i:236739 original size:39 final size:40
Alignment explanation
Indices: 236589--236725 Score: 130
Period size: 40 Copynumber: 3.6 Consensus size: 40
236579 CAATGATTTT
*
236589 TTTTTACAAAATA-AGAAAATAAATCCAACGATTTA-TTCC
1 TTTTTACAAAATAGA-AAAATAAATCAAACGATTTATTTCC
* * *
236628 ---CTA-AAACA-AG-AAAATAAATCGAACGAGTTATTTCC
1 TTTTTACAAA-ATAGAAAAATAAATCAAACGATTTATTTCC
* *
236663 TTTTTACAAAATAGAAAAATCAATCAAACGATCTATTTCC
1 TTTTTACAAAATAGAAAAATAAATCAAACGATTTATTTCC
*
236703 TTTTT-CAAAATAGGAAAATAAAT
1 TTTTTACAAAATAGAAAAATAAAT
236726 TCTACTATTT
Statistics
Matches: 79, Mismatches: 10, Indels: 18
0.74 0.09 0.17
Matches are distributed among these distances:
34 18 0.23
35 8 0.10
36 3 0.04
38 3 0.04
39 21 0.27
40 26 0.33
ACGTcount: A:0.47, C:0.15, G:0.07, T:0.31
Consensus pattern (40 bp):
TTTTTACAAAATAGAAAAATAAATCAAACGATTTATTTCC
Found at i:236837 original size:137 final size:136
Alignment explanation
Indices: 236637--236942 Score: 402
Period size: 137 Copynumber: 2.2 Consensus size: 136
236627 CCTAAAACAA
* *
236637 GAAAATAAA-TCGAACGAGTTATTTCCTTTTTACAAAATAGAAAAATCAATCAAACGATCTATTT
1 GAAAATAAATTC-AACGATTTATTTCC-TTTTACAAAATAGAAAAATAAATCAAAC-ATCTATTT
* * * * * *
236701 CCTTTTTC-AAAATAGGAAAATAAATTCTACTATTTATTTTTCTTTTACATATCAGAATCATATA
63 CCTTTTACAAAAATAGGAAAATAAATCCAACGATTTA-TTTCCTTTTACAGATCAGAATCATATA
236765 AGATTCTTAG
127 AGATTCTTAG
* * *
236775 GAAAATAAATTTAACAATTTATTTCCTTTTACAAAATAGAAAAATAAATTCAATA-ATTTATTTC
1 GAAAATAAATTCAACGATTTATTTCCTTTTACAAAATAGAAAAATAAA-TCAA-ACATCTATTTC
* *
236839 CTTTTACAAAAATAGGAAAATAAATCCAACGATTTATTTCCTTTTACAGATCAGAATCATGTGAG
64 CTTTTACAAAAATAGGAAAATAAATCCAACGATTTATTTCCTTTTACAGATCAGAATCATATAAG
236904 ATTCTTAG
129 ATTCTTAG
* *
236912 GAAAATAAATTCAACGCTTTATCTCCTTTTA
1 GAAAATAAATTCAACGATTTATTTCCTTTTA
236943 AAAGATAAAA
Statistics
Matches: 147, Mismatches: 17, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
137 95 0.65
138 50 0.34
139 2 0.01
ACGTcount: A:0.41, C:0.14, G:0.08, T:0.37
Consensus pattern (136 bp):
GAAAATAAATTCAACGATTTATTTCCTTTTACAAAATAGAAAAATAAATCAAACATCTATTTCCT
TTTACAAAAATAGGAAAATAAATCCAACGATTTATTTCCTTTTACAGATCAGAATCATATAAGAT
TCTTAG
Found at i:236862 original size:40 final size:40
Alignment explanation
Indices: 236772--236886 Score: 178
Period size: 40 Copynumber: 2.9 Consensus size: 40
236762 ATAAGATTCT
*
236772 TAGGAAAATAAATTTAACAATTTATTTCCTTTTAC-AAAA
1 TAGGAAAATAAATTCAACAATTTATTTCCTTTTACAAAAA
* *
236811 TAGAAAAATAAATTCAATAATTTATTTCCTTTTACAAAAA
1 TAGGAAAATAAATTCAACAATTTATTTCCTTTTACAAAAA
* *
236851 TAGGAAAATAAATCCAACGATTTATTTCCTTTTACA
1 TAGGAAAATAAATTCAACAATTTATTTCCTTTTACA
236887 GATCAGAATC
Statistics
Matches: 68, Mismatches: 7, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
39 32 0.47
40 36 0.53
ACGTcount: A:0.45, C:0.12, G:0.05, T:0.37
Consensus pattern (40 bp):
TAGGAAAATAAATTCAACAATTTATTTCCTTTTACAAAAA
Found at i:237105 original size:58 final size:58
Alignment explanation
Indices: 236992--237267 Score: 238
Period size: 58 Copynumber: 5.0 Consensus size: 58
236982 TTTCTTTATT
* * * * ** * *
236992 CAAGATTCCCGAGAAAATAAATTTAACAATTTATTTCTTTTTA-AAGGATAGAATCATC
1 CAAGATTCTCAAGGAAATAAATTCAACAATTTATTT-TCCTTACAAAGTTAGAATCATC
* * * * *
237050 CACGATTCTCAAGAAAATAAATTCGACAATTTATTTTCCTTACAAAGTTAAAATCATT
1 CAAGATTCTCAAGGAAATAAATTCAACAATTTATTTTCCTTACAAAGTTAGAATCATC
* * *
237108 CAAGGTTCTCAAGGAAATAAATTCAAC-A---A-------TACAAGGTTAGAATCATT
1 CAAGATTCTCAAGGAAATAAATTCAACAATTTATTTTCCTTACAAAGTTAGAATCATC
* * * *
237155 CTAGATTCTCAAGGAAACAAA-TCAACGATTTATTTTTCTTACAAAGTTAGAATCAAT-
1 CAAGATTCTCAAGGAAATAAATTCAACAATTTATTTTCCTTACAAAGTTAGAATC-ATC
* *
237212 CAAGATTCTCAAGGAAATAAATTCAACAATTTTTTTTCCTTACGAAGTTAGAATCA
1 CAAGATTCTCAAGGAAATAAATTCAACAATTTATTTTCCTTACAAAGTTAGAATCA
237268 ACGCAAATCC
Statistics
Matches: 177, Mismatches: 27, Indels: 29
0.76 0.12 0.12
Matches are distributed among these distances:
46 5 0.03
47 35 0.20
50 1 0.01
54 1 0.01
57 39 0.22
58 96 0.54
ACGTcount: A:0.41, C:0.16, G:0.11, T:0.33
Consensus pattern (58 bp):
CAAGATTCTCAAGGAAATAAATTCAACAATTTATTTTCCTTACAAAGTTAGAATCATC
Found at i:237152 original size:47 final size:46
Alignment explanation
Indices: 237090--237180 Score: 128
Period size: 47 Copynumber: 2.0 Consensus size: 46
237080 TTATTTTCCT
* *
237090 TACAAAGTTAAAATCATTCAAGGTTCTCAAGGAAATAAATTCAACAA
1 TACAAAGTTAAAATCATTCAAGATTCTCAAGGAAACAAA-TCAACAA
* * *
237137 TACAAGGTTAGAATCATTCTAGATTCTCAAGGAAACAAATCAAC
1 TACAAAGTTAAAATCATTCAAGATTCTCAAGGAAACAAATCAAC
237181 GATTTATTTT
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
46 5 0.13
47 34 0.87
ACGTcount: A:0.46, C:0.16, G:0.12, T:0.25
Consensus pattern (46 bp):
TACAAAGTTAAAATCATTCAAGATTCTCAAGGAAACAAATCAACAA
Found at i:237206 original size:57 final size:58
Alignment explanation
Indices: 237137--237268 Score: 187
Period size: 57 Copynumber: 2.3 Consensus size: 58
237127 AATTCAACAA
* * * *
237137 TACAAGGTTAGAATCATTCTAGATTCTCAAGGAAACAAA-TCAACGATTTATTTTT-CT
1 TACAAAGTTAGAATCAATCAAGATTCTCAAGGAAACAAATTCAACAATTT-TTTTTCCT
*
237194 TACAAAGTTAGAATCAATCAAGATTCTCAAGGAAATAAATTCAACAATTTTTTTTCCT
1 TACAAAGTTAGAATCAATCAAGATTCTCAAGGAAACAAATTCAACAATTTTTTTTCCT
*
237252 TACGAAGTTAGAATCAA
1 TACAAAGTTAGAATCAA
237269 CGCAAATCCT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
57 40 0.60
58 27 0.40
ACGTcount: A:0.40, C:0.15, G:0.11, T:0.33
Consensus pattern (58 bp):
TACAAAGTTAGAATCAATCAAGATTCTCAAGGAAACAAATTCAACAATTTTTTTTCCT
Found at i:237221 original size:104 final size:105
Alignment explanation
Indices: 237035--237241 Score: 301
Period size: 104 Copynumber: 2.0 Consensus size: 105
237025 TTTCTTTTTA
* *
237035 AAGGATAGAATCATCCACGATTCTCAAGAAAATAAATTCGACAATTTATTTTCCTTACAAAGTTA
1 AAGGATAGAATCATCCACGATTCTCAAGAAAACAAATTCAACAATTTATTTTCCTTACAAAGTTA
* *
237100 AAATCATTCAAGGTTCTCAAGGAAATAAATTCAACAATAC
66 AAATCAATCAAGATTCTCAAGGAAATAAATTCAACAATAC
* * * * *
237140 AAGGTTAGAATCATTCTA-GATTCTCAAGGAAACAAA-TCAACGATTTATTTTTCTTACAAAGTT
1 AAGGATAGAATCA-TCCACGATTCTCAAGAAAACAAATTCAACAATTTATTTTCCTTACAAAGTT
*
237203 AGAATCAATCAAGATTCTCAAGGAAATAAATTCAACAAT
65 AAAATCAATCAAGATTCTCAAGGAAATAAATTCAACAAT
237242 TTTTTTTCCT
Statistics
Matches: 91, Mismatches: 10, Indels: 3
0.88 0.10 0.03
Matches are distributed among these distances:
104 60 0.66
105 28 0.31
106 3 0.03
ACGTcount: A:0.43, C:0.16, G:0.11, T:0.29
Consensus pattern (105 bp):
AAGGATAGAATCATCCACGATTCTCAAGAAAACAAATTCAACAATTTATTTTCCTTACAAAGTTA
AAATCAATCAAGATTCTCAAGGAAATAAATTCAACAATAC
Found at i:237481 original size:42 final size:44
Alignment explanation
Indices: 237422--237526 Score: 124
Period size: 45 Copynumber: 2.4 Consensus size: 44
237412 TAAATTTTAC
* * * *
237422 TAACCCAATAATCAAAAAG-A-AACCATTTGCTTTTACTTTTGG
1 TAACCCAATAATAAAAAAGAACAACCATTCGATTTTACTTTTGA
* *
237464 TAACACAATAATAAAAAAGAACTAATCATTCGATTTTACTTTTGA
1 TAACCCAATAATAAAAAAGAAC-AACCATTCGATTTTACTTTTGA
*
237509 CAACCCAATAATAAAAAA
1 TAACCCAATAATAAAAAA
237527 CCTTGGATTC
Statistics
Matches: 52, Mismatches: 8, Indels: 3
0.83 0.13 0.05
Matches are distributed among these distances:
42 17 0.33
43 1 0.02
45 34 0.65
ACGTcount: A:0.47, C:0.17, G:0.07, T:0.30
Consensus pattern (44 bp):
TAACCCAATAATAAAAAAGAACAACCATTCGATTTTACTTTTGA
Found at i:247159 original size:21 final size:21
Alignment explanation
Indices: 247133--247180 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
247123 GTTTCCAGAT
*
247133 TCGCAACGCGAACATCGACTA
1 TCGCAACGCGAACATCGACCA
* *
247154 TCGCAACGCGAACTTCTACCA
1 TCGCAACGCGAACATCGACCA
247175 TCGCAA
1 TCGCAA
247181 TGTGATTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.31, C:0.35, G:0.17, T:0.17
Consensus pattern (21 bp):
TCGCAACGCGAACATCGACCA
Found at i:247999 original size:6 final size:6
Alignment explanation
Indices: 247990--248014 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
247980 CGCCGCCGTC
247990 TCGTGG TCGTGG TCGTGG TCGTGG T
1 TCGTGG TCGTGG TCGTGG TCGTGG T
248015 AATACGTGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.16, G:0.48, T:0.36
Consensus pattern (6 bp):
TCGTGG
Found at i:258876 original size:32 final size:33
Alignment explanation
Indices: 258780--258878 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
258770 AACTCAACAT
* * *
258780 AATTGAAATACTTAAATACTTCCAAGTTTGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
258813 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
258846 AATTCAAATACTTAAAAACTT-CAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
258878 A
1 A
258879 TTGAAACAAA
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 12 0.19
33 51 0.81
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.32
Consensus pattern (33 bp):
AATTCAAATACTTAAAAACTTCCAAGTTCGATA
Found at i:258897 original size:21 final size:21
Alignment explanation
Indices: 258873--258914 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
258863 ACTTCAAGTT
258873 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
*
258894 CGATAATTGAAATAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
258915 AAAATAAACT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.48, C:0.07, G:0.14, T:0.31
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTA
Found at i:261372 original size:27 final size:28
Alignment explanation
Indices: 261335--261392 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
261325 AAAAAACCGG
261335 TTTTTCCC-AAATCCGAT-TTCGGATATT
1 TTTTTCCCAAAATCCGATATTCGGAT-TT
* *
261362 TTTTTCGCAAAATCGGATATTCGGATTT
1 TTTTTCCCAAAATCCGATATTCGGATTT
261390 TTT
1 TTT
261393 GTGCACCCCT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
27 7 0.26
28 13 0.48
29 7 0.26
ACGTcount: A:0.22, C:0.17, G:0.14, T:0.47
Consensus pattern (28 bp):
TTTTTCCCAAAATCCGATATTCGGATTT
Found at i:262862 original size:13 final size:13
Alignment explanation
Indices: 262844--262868 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
262834 TAGGTAATAA
262844 AACACAAATGAAG
1 AACACAAATGAAG
262857 AACACAAATGAA
1 AACACAAATGAA
262869 TCCAAGCGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.16, G:0.12, T:0.08
Consensus pattern (13 bp):
AACACAAATGAAG
Found at i:266854 original size:20 final size:20
Alignment explanation
Indices: 266829--267117 Score: 216
Period size: 20 Copynumber: 14.7 Consensus size: 20
266819 GATTTTCCAT
* *
266829 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGAATACGTA
* **
266849 AATCGCAACGCGAACATATA
1 AATCGCAACGCGAATACGTA
*
266869 AATCGCAACGCG-ATTC-TGA
1 AATCGCAACGCGAATACGT-A
* * * * *
266888 CTATCACAACGAGTATCCGTAA
1 -AATCGCAACGCGAATACGT-A
* *
266910 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATACGTA
*
266930 AATCGCAACGAGAATACGTAA
1 AATCGCAACGCGAATACGT-A
* * *
266951 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGAATACGTA
*
266971 AATCGCAACGAGAATACGTA
1 AATCGCAACGCGAATACGTA
*
266991 AATCGTAACGCG-----G-A
1 AATCGCAACGCGAATACGTA
* *
267005 AATCACAACGAGAATACGTA
1 AATCGCAACGCGAATACGTA
* * *
267025 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGAATACGTA
*
267045 AATCGCAATGCGAATACGTA
1 AATCGCAACGCGAATACGTA
*
267065 AATCGCAATGCGAATACGTA
1 AATCGCAACGCGAATACGTA
** * *
267085 AATCGCAATTCGTATCCGTA
1 AATCGCAACGCGAATACGTA
267105 AATCGCAACGCGA
1 AATCGCAACGCGA
267118 TTTTTAAAGC
Statistics
Matches: 217, Mismatches: 41, Indels: 22
0.77 0.15 0.08
Matches are distributed among these distances:
14 10 0.05
15 1 0.00
18 1 0.00
19 3 0.01
20 164 0.76
21 36 0.17
22 2 0.01
ACGTcount: A:0.38, C:0.24, G:0.19, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGAATACGTA
Found at i:266921 original size:41 final size:41
Alignment explanation
Indices: 266890--267088 Score: 218
Period size: 41 Copynumber: 5.1 Consensus size: 41
266880 GATTCTGACT
* *
266890 ATCACAACGAGTATCCGTAAAATCGCAACGCGTATCCGTAA
1 ATCACAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
* *
266931 ATCGCAACGAGAATACGTAAAATCGCAACGTGTATCCGTAA
1 ATCACAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
* *
266972 ATCGCAACGAGAATACGT-AAATCGTAACGCG-----G-AA
1 ATCACAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
*
267006 ATCACAACGAGAATACGT-AAATCGCAATGCGTATCCGTAA
1 ATCACAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
* * * * * *
267046 ATCGCAATGCGAATACGT-AAATCGCAATGCGAATACGTAA
1 ATCACAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
267086 ATC
1 ATC
267089 GCAATTCGTA
Statistics
Matches: 138, Mismatches: 14, Indels: 13
0.84 0.08 0.08
Matches are distributed among these distances:
34 30 0.22
35 1 0.01
39 1 0.01
40 51 0.37
41 55 0.40
ACGTcount: A:0.39, C:0.23, G:0.19, T:0.19
Consensus pattern (41 bp):
ATCACAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
Found at i:267051 original size:74 final size:75
Alignment explanation
Indices: 266929--267069 Score: 230
Period size: 74 Copynumber: 1.9 Consensus size: 75
266919 GCGTATCCGT
* *
266929 AAATCGCAACGAGAATACGTAAAATCGCAACGTGTATCCGTAAATCGCAACGAGAATACGTAAAT
1 AAATCACAACGAGAATACGTAAAATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGTAAAT
266994 CGTAACGCGG
66 CGTAACGCGG
* * *
267004 AAATCACAACGAGAATACGT-AAATCGCAATGCGTATCCGTAAATCGCAATGCGAATACGTAAAT
1 AAATCACAACGAGAATACGTAAAATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGTAAAT
267068 CG
66 CG
267070 CAATGCGAAT
Statistics
Matches: 61, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
74 42 0.69
75 19 0.31
ACGTcount: A:0.40, C:0.21, G:0.20, T:0.18
Consensus pattern (75 bp):
AAATCACAACGAGAATACGTAAAATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGTAAAT
CGTAACGCGG
Found at i:267696 original size:21 final size:21
Alignment explanation
Indices: 267636--267714 Score: 76
Period size: 20 Copynumber: 3.9 Consensus size: 21
267626 TTCTAAACTT
267636 AAAATCGCAAC-ATGA-AAATG
1 AAAATCGCAACGA-GAGAAATG
*
267656 AAAATCGGAAC-ACGA-AAATG
1 AAAATCGCAACGA-GAGAAATG
**
267676 ACTATCGCAACGAGAGAAATG
1 AAAATCGCAACGAGAGAAATG
*
267697 AAAATCGTAACGAGAGAA
1 AAAATCGCAACGAGAGAA
267715 TCGCAACGCG
Statistics
Matches: 49, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
20 28 0.57
21 21 0.43
ACGTcount: A:0.52, C:0.15, G:0.20, T:0.13
Consensus pattern (21 bp):
AAAATCGCAACGAGAGAAATG
Found at i:267742 original size:33 final size:33
Alignment explanation
Indices: 267705--267768 Score: 110
Period size: 33 Copynumber: 1.9 Consensus size: 33
267695 TGAAAATCGT
*
267705 AACGAGAGAATCGCAACGCGAAGCCAAAATCAC
1 AACGAGAGAATCGCAACGCGAAACCAAAATCAC
*
267738 AACGAGATAATCGCAACGCGAAACCAAAATC
1 AACGAGAGAATCGCAACGCGAAACCAAAATC
267769 GTATTGCGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.47, C:0.27, G:0.19, T:0.08
Consensus pattern (33 bp):
AACGAGAGAATCGCAACGCGAAACCAAAATCAC
Found at i:267794 original size:19 final size:19
Alignment explanation
Indices: 267772--267912 Score: 115
Period size: 19 Copynumber: 7.8 Consensus size: 19
267762 CAAAATCGTA
267772 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCG
*
267791 TTGCGATTTTAATTTCGCG
1 TTGCGATTTTCATTTCGCG
*
267810 TTGCGA--TTC---TCTCG
1 TTGCGATTTTCATTTCGCG
*
267824 TTGTGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCG
*
267843 TTGCGA--TTC---TCTCG
1 TTGCGATTTTCATTTCGCG
**
267857 TTGCGATAGTCATTTC-CATG
1 TTGCGATTTTCATTTCGC--G
*
267877 TTGCGATTTTCATTCTCTCG
1 TTGCGATTTTCATT-TCGCG
267897 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
267913 AACCAAAAGA
Statistics
Matches: 98, Mismatches: 10, Indels: 28
0.72 0.07 0.21
Matches are distributed among these distances:
14 19 0.19
16 5 0.05
17 5 0.05
18 1 0.01
19 37 0.38
20 28 0.29
21 2 0.02
22 1 0.01
ACGTcount: A:0.12, C:0.21, G:0.19, T:0.48
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCG
Found at i:267832 original size:33 final size:33
Alignment explanation
Indices: 267789--267863 Score: 132
Period size: 33 Copynumber: 2.3 Consensus size: 33
267779 TTTCATTTCG
267789 CGTTGCGATTTTAATTTCGCGTTGCGATTCTCT
1 CGTTGCGATTTTAATTTCGCGTTGCGATTCTCT
* *
267822 CGTTGTGATTTTCATTTCGCGTTGCGATTCTCT
1 CGTTGCGATTTTAATTTCGCGTTGCGATTCTCT
267855 CGTTGCGAT
1 CGTTGCGAT
267864 AGTCATTTCC
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.45
Consensus pattern (33 bp):
CGTTGCGATTTTAATTTCGCGTTGCGATTCTCT
Found at i:267870 original size:33 final size:33
Alignment explanation
Indices: 267802--267872 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
267792 TGCGATTTTA
* **
267802 ATTTCGCGTTGCGATTCTCTCGTTGTGATTTTC
1 ATTTCGCGTTGCGATTCTCTCGTTGCGATAGTC
267835 ATTTCGCGTTGCGATTCTCTCGTTGCGATAGTC
1 ATTTCGCGTTGCGATTCTCTCGTTGCGATAGTC
267868 ATTTC
1 ATTTC
267873 CATGTTGCGA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.21, T:0.45
Consensus pattern (33 bp):
ATTTCGCGTTGCGATTCTCTCGTTGCGATAGTC
Found at i:267889 original size:20 final size:21
Alignment explanation
Indices: 267849--267912 Score: 80
Period size: 20 Copynumber: 3.1 Consensus size: 21
267839 CGCGTTGCGA
**
267849 TTCTCTCGTTGCGATAGTCAT
1 TTCTCTCGTTGCGATTTTCAT
267870 TTC-CAT-GTTGCGATTTTCA-
1 TTCTC-TCGTTGCGATTTTCAT
267889 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
267910 TTC
1 TTC
267913 AACCAAAAGA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
19 4 0.11
20 26 0.70
21 7 0.19
ACGTcount: A:0.12, C:0.23, G:0.16, T:0.48
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:268033 original size:25 final size:26
Alignment explanation
Indices: 267979--268033 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 26
267969 TTATGTTTAT
*
267979 TGTTTTTGGTATATCTTCACAGTGTA
1 TGTTTTTGGTATATCTTAACAGTGTA
**
268005 -GTTTTTGGTATATC-TAACTTTGTA
1 TGTTTTTGGTATATCTTAACAGTGTA
268029 TGTTT
1 TGTTT
268034 ATTGTTTTTG
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
24 7 0.28
25 18 0.72
ACGTcount: A:0.18, C:0.09, G:0.18, T:0.55
Consensus pattern (26 bp):
TGTTTTTGGTATATCTTAACAGTGTA
Found at i:269856 original size:21 final size:21
Alignment explanation
Indices: 269832--269898 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
269822 TCATTCCTCG
269832 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
269853 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
269874 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
269895 AGAG
1 AGAG
269899 CCCAATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:269856 original size:42 final size:42
Alignment explanation
Indices: 269780--269898 Score: 107
Period size: 42 Copynumber: 2.8 Consensus size: 42
269770 GACTCGCCTG
* * * * * * *
269780 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
*
269822 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTG
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
* * *
269864 TCA-TCGTTGAAGAGGT-CCCTCCCACCATTCAAGAG
1 TCATTCCTCG-AGA-GTCCCCTCCCACCGTTCAAGAG
269899 CCCAATTCAC
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
41 4 0.06
42 58 0.91
43 2 0.03
ACGTcount: A:0.23, C:0.36, G:0.18, T:0.23
Consensus pattern (42 bp):
TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
Found at i:271265 original size:14 final size:14
Alignment explanation
Indices: 271246--271281 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
271236 ATTGTTTAAT
271246 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
271260 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
271274 TGATTTGT
1 TGATTTGT
271282 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:271430 original size:33 final size:32
Alignment explanation
Indices: 271388--271486 Score: 117
Period size: 33 Copynumber: 3.0 Consensus size: 32
271378 AAAAATGACT
* *
271388 ATCGCAATGCGAAATGAAAATCACAACGAGAGA
1 ATCGCAATGCGAAAT-AAAATCGCAACGAGAAA
* *
271421 ATCGCAATGCGAAATTAAAATCGTAACGATAAA
1 ATCGCAATGCGAAA-TAAAATCGCAACGAGAAA
* *
271454 ATCGCAACGCGAAACTAAAATCGCAACGCGAAA
1 ATCGCAATGCGAAA-TAAAATCGCAACGAGAAA
271487 CTAAATTTGC
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
33 55 0.98
34 1 0.02
ACGTcount: A:0.47, C:0.20, G:0.18, T:0.14
Consensus pattern (32 bp):
ATCGCAATGCGAAATAAAATCGCAACGAGAAA
Found at i:271474 original size:19 final size:19
Alignment explanation
Indices: 271450--271491 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
271440 ATCGTAACGA
271450 TAAAATCGCAACGCGAAAC
1 TAAAATCGCAACGCGAAAC
271469 TAAAATCGCAACGCGAAAC
1 TAAAATCGCAACGCGAAAC
271488 TAAA
1 TAAA
271492 TTTGCGTTGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.50, C:0.24, G:0.14, T:0.12
Consensus pattern (19 bp):
TAAAATCGCAACGCGAAAC
Found at i:271555 original size:19 final size:19
Alignment explanation
Indices: 271531--271610 Score: 80
Period size: 19 Copynumber: 4.4 Consensus size: 19
271521 GATTCCCTCG
271531 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
** *
271550 TTGCGATAGTCATTTCCGCG
1 TTGCGATTTTCATTT-CGCA
271570 TTGCGATTTTCA---CG--
1 TTGCGATTTTCATTTCGCA
*
271584 TTGCGATTTTCATTTTGCA
1 TTGCGATTTTCATTTCGCA
271603 TTGCGATT
1 TTGCGATT
271611 CTCTCGTTGC
Statistics
Matches: 49, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
14 12 0.24
16 2 0.04
17 1 0.02
19 21 0.43
20 13 0.27
ACGTcount: A:0.15, C:0.20, G:0.20, T:0.45
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:271601 original size:14 final size:14
Alignment explanation
Indices: 271568--271595 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
271558 GTCATTTCCG
271568 CGTTGCGATTTTCA
1 CGTTGCGATTTTCA
271582 CGTTGCGATTTTCA
1 CGTTGCGATTTTCA
271596 TTTTGCATTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.21, G:0.21, T:0.43
Consensus pattern (14 bp):
CGTTGCGATTTTCA
Found at i:271689 original size:20 final size:20
Alignment explanation
Indices: 271616--271689 Score: 62
Period size: 20 Copynumber: 3.6 Consensus size: 20
271606 CGATTCTCTC
* *
271616 GTTGCGATAGTAATTTCCGC
1 GTTGCGATAGTCATTTCCGT
* **
271636 GTTGCGATAGACA-TTAAGAT
1 GTTGCGATAGTCATTTCCG-T
271656 GATTGCGA-ACGTCATTTCCGT
1 G-TTGCGATA-GTCATTTCCGT
271677 GTTGCGATAGTCA
1 GTTGCGATAGTCA
271690 AATGAATGCC
Statistics
Matches: 41, Mismatches: 8, Indels: 10
0.69 0.14 0.17
Matches are distributed among these distances:
19 3 0.07
20 23 0.56
21 12 0.29
22 3 0.07
ACGTcount: A:0.24, C:0.18, G:0.26, T:0.32
Consensus pattern (20 bp):
GTTGCGATAGTCATTTCCGT
Found at i:275190 original size:34 final size:36
Alignment explanation
Indices: 275107--275289 Score: 154
Period size: 41 Copynumber: 4.8 Consensus size: 36
275097 CGTATTCGCA
* * *
275107 TTGCGATTTACGTATTCGCTTTGCGATTTACGGATACGCA
1 TTGCGATTTACGTATTCTCGTTGCGATTTAC----ACGCG
*
275147 TTGCGATTTACGTATTCTCGTTGTGATTT-C-CGCG
1 TTGCGATTTACGTATTCTCGTTGCGATTTACACGCG
*
275181 TTGCGATTTACATATTCTCGTTGCGATTTACGGATACGCG
1 TTGCGATTTACGTATTCTCGTTGCGATTTAC----ACGCG
275221 TTGCGATTTTACGTATTCTCGTTGCGATTTACGGATACGCG
1 TTGCGA-TTTACGTATTCTCGTTGCGATTTAC----ACGCG
* * *
275262 TTGCGATTTTACGGATACTCGTTACGAT
1 TTGCGA-TTTACGTATTCTCGTTGCGAT
275290 AGTCAGAATT
Statistics
Matches: 126, Mismatches: 10, Indels: 13
0.85 0.07 0.09
Matches are distributed among these distances:
34 30 0.24
35 1 0.01
39 1 0.01
40 36 0.29
41 58 0.46
ACGTcount: A:0.18, C:0.20, G:0.23, T:0.39
Consensus pattern (36 bp):
TTGCGATTTACGTATTCTCGTTGCGATTTACACGCG
Found at i:275211 original size:74 final size:75
Alignment explanation
Indices: 275107--275250 Score: 236
Period size: 74 Copynumber: 1.9 Consensus size: 75
275097 CGTATTCGCA
* * *
275107 TTGCGATTTACGTATTCGCTTTGCGATTTACGGATACGCATTGCGA-TTTACGTATTCTCGTTGT
1 TTGCGATTTACATATTCGCGTTGCGATTTACGGATACGCATTGCGATTTTACGTATTCTCGTTGC
275171 GATTTCCGCG
66 GATTTCCGCG
* *
275181 TTGCGATTTACATATTCTCGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCTCGTTGC
1 TTGCGATTTACATATTCGCGTTGCGATTTACGGATACGCATTGCGATTTTACGTATTCTCGTTGC
275246 GATTT
66 GATTT
275251 ACGGATACGC
Statistics
Matches: 64, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
74 42 0.66
75 22 0.34
ACGTcount: A:0.17, C:0.19, G:0.22, T:0.42
Consensus pattern (75 bp):
TTGCGATTTACATATTCGCGTTGCGATTTACGGATACGCATTGCGATTTTACGTATTCTCGTTGC
GATTTCCGCG
Found at i:275233 original size:21 final size:20
Alignment explanation
Indices: 275065--275289 Score: 174
Period size: 20 Copynumber: 11.4 Consensus size: 20
275055 GTCAGAATCT
* *
275065 CGTTGCGATTTACAGATTCG
1 CGTTGCGATTTACGGATACG
* * * *
275085 CATTGTGATTTACGTATTCG
1 CGTTGCGATTTACGGATACG
* * *
275105 CATTGCGATTTACGTATTCG
1 CGTTGCGATTTACGGATACG
*
275125 CTTTGCGATTTACGGATACG
1 CGTTGCGATTTACGGATACG
* * * *
275145 CATTGCGATTTACGTATTCT
1 CGTTGCGATTTACGGATACG
*
275165 CGTTGTGATTT-C-----CG
1 CGTTGCGATTTACGGATACG
** * *
275179 CGTTGCGATTTACATATTCT
1 CGTTGCGATTTACGGATACG
275199 CGTTGCGATTTACGGATACG
1 CGTTGCGATTTACGGATACG
* * *
275219 CGTTGCGATTTTACGTATTCT
1 CGTTGCGA-TTTACGGATACG
275240 CGTTGCGATTTACGGATACG
1 CGTTGCGATTTACGGATACG
*
275260 CGTTGCGATTTTACGGATACT
1 CGTTGCGA-TTTACGGATACG
*
275281 CGTTACGAT
1 CGTTGCGAT
275290 AGTCAGAATT
Statistics
Matches: 168, Mismatches: 29, Indels: 16
0.79 0.14 0.08
Matches are distributed among these distances:
14 11 0.07
15 1 0.01
19 1 0.01
20 120 0.71
21 35 0.21
ACGTcount: A:0.19, C:0.20, G:0.23, T:0.39
Consensus pattern (20 bp):
CGTTGCGATTTACGGATACG
Found at i:275241 original size:41 final size:40
Alignment explanation
Indices: 275065--275289 Score: 248
Period size: 40 Copynumber: 5.7 Consensus size: 40
275055 GTCAGAATCT
* * * * *
275065 CGTTGCGATTTACAG-ATTCGCATTGTGATTTACGTATTCG
1 CGTTGCGATTTAC-GTATTCTCGTTGCGATTTACGGATACG
* * *
275105 CATTGCGATTTACGTATTCGCTTTGCGATTTACGGATACG
1 CGTTGCGATTTACGTATTCTCGTTGCGATTTACGGATACG
* *
275145 CATTGCGATTTACGTATTCTCGTTGTGATTT-C-----CG
1 CGTTGCGATTTACGTATTCTCGTTGCGATTTACGGATACG
*
275179 CGTTGCGATTTACATATTCTCGTTGCGATTTACGGATACG
1 CGTTGCGATTTACGTATTCTCGTTGCGATTTACGGATACG
275219 CGTTGCGATTTTACGTATTCTCGTTGCGATTTACGGATACG
1 CGTTGCGA-TTTACGTATTCTCGTTGCGATTTACGGATACG
* * *
275260 CGTTGCGATTTTACGGATACTCGTTACGAT
1 CGTTGCGA-TTTACGTATTCTCGTTGCGAT
275290 AGTCAGAATT
Statistics
Matches: 162, Mismatches: 15, Indels: 15
0.84 0.08 0.08
Matches are distributed among these distances:
34 30 0.19
35 1 0.01
39 2 0.01
40 71 0.44
41 58 0.36
ACGTcount: A:0.19, C:0.20, G:0.23, T:0.39
Consensus pattern (40 bp):
CGTTGCGATTTACGTATTCTCGTTGCGATTTACGGATACG
Found at i:275323 original size:20 final size:20
Alignment explanation
Indices: 275300--275350 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
275290 AGTCAGAATT
*
275300 GCGTTGCGATTTAT-ATGTTC
1 GCGTTGCGATTT-TCATATTC
275320 GCGTTGCGATTTTCATATTC
1 GCGTTGCGATTTTCATATTC
*
275340 GCATTGCGATT
1 GCGTTGCGATT
275351 ATGGAAAATC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 1 0.04
20 27 0.96
ACGTcount: A:0.16, C:0.18, G:0.24, T:0.43
Consensus pattern (20 bp):
GCGTTGCGATTTTCATATTC
Found at i:275332 original size:61 final size:61
Alignment explanation
Indices: 275177--275332 Score: 156
Period size: 61 Copynumber: 2.5 Consensus size: 61
275167 TTGTGATTTC
* * * * * *
275177 CGCGTTGCGATTTACATATTCTCGTTGCGA-TTTACGGATACGCGTTGCGATTTTACGTATT
1 CGCGTTGCGATTTA-ATGTTCGCGTTGCGATTTTACGGATACGCGTTACGATGTCACGAATT
* ** * *
275238 CTCGTTGCGATTTACGGATACGCGTTGCGATTTTACGGATACTCGTTACGATAGTCA-GAATT
1 CGCGTTGCGATTTAATG-TTCGCGTTGCGATTTTACGGATACGCGTTACGAT-GTCACGAATT
275300 -GCGTTGCGATTTATATGTTCGCGTTGCGATTTT
1 CGCGTTGCGATTTA-ATGTTCGCGTTGCGATTTT
275333 CATATTCGCA
Statistics
Matches: 76, Mismatches: 15, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
61 50 0.66
62 24 0.32
63 2 0.03
ACGTcount: A:0.19, C:0.19, G:0.24, T:0.38
Consensus pattern (61 bp):
CGCGTTGCGATTTAATGTTCGCGTTGCGATTTTACGGATACGCGTTACGATGTCACGAATT
Found at i:275403 original size:21 final size:20
Alignment explanation
Indices: 275318--275413 Score: 70
Period size: 21 Copynumber: 4.7 Consensus size: 20
275308 ATTTATATGT
* *
275318 TCGCGTTGCGATTTTCATAT
1 TCGCATTGCGATTTTCATAA
** *
275338 TCGCATTGCGATTATGGAAAA
1 TCGCATTGCGATT-TTCATAA
*
275359 TCGCAATGCGAATTTGT-ACT-A
1 TCGCATTGCG-ATTT-TCA-TAA
275380 TCGCATTGCGATTATTCATAA
1 TCGCATTGCGATT-TTCATAA
*
275401 TCGCGTTGCGATT
1 TCGCATTGCGATT
275414 CTGGGAACTG
Statistics
Matches: 59, Mismatches: 10, Indels: 13
0.72 0.12 0.16
Matches are distributed among these distances:
20 17 0.29
21 39 0.66
22 3 0.05
ACGTcount: A:0.24, C:0.19, G:0.21, T:0.36
Consensus pattern (20 bp):
TCGCATTGCGATTTTCATAA
Found at i:275411 original size:42 final size:42
Alignment explanation
Indices: 275318--275411 Score: 104
Period size: 42 Copynumber: 2.3 Consensus size: 42
275308 ATTTATATGT
*
275318 TCGCGTTGCG-ATTTTCATATTCGCATTGCGATTATGGAAAA
1 TCGCGTTGCGAATTTTCATATTCGCATTGCGATTATGCAAAA
** * *
275359 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTATTCATAA
1 TCGCGTTGCGAATTT-TCA-TATTCGCATTGCGATTATGCAAAA
275401 TCGCGTTGCGA
1 TCGCGTTGCGA
275412 TTCTGGGAAC
Statistics
Matches: 43, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
41 8 0.19
42 32 0.74
43 3 0.07
ACGTcount: A:0.24, C:0.19, G:0.21, T:0.35
Consensus pattern (42 bp):
TCGCGTTGCGAATTTTCATATTCGCATTGCGATTATGCAAAA
Found at i:275856 original size:20 final size:19
Alignment explanation
Indices: 275810--275857 Score: 78
Period size: 19 Copynumber: 2.5 Consensus size: 19
275800 ATGACCAACA
*
275810 AAATCGCAATGCGATCTCT
1 AAATCGCAATGCGATCTCC
275829 AAATCGCAATGCGATCTCC
1 AAATCGCAATGCGATCTCC
275848 AATATCGCAA
1 AA-ATCGCAA
275858 ATCAGTTTCC
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
19 20 0.74
20 7 0.26
ACGTcount: A:0.35, C:0.27, G:0.15, T:0.23
Consensus pattern (19 bp):
AAATCGCAATGCGATCTCC
Found at i:275895 original size:20 final size:20
Alignment explanation
Indices: 275872--275943 Score: 83
Period size: 20 Copynumber: 3.6 Consensus size: 20
275862 GTTTCCAGAT
*
275872 TCGCAACGCGATTTTGACTA
1 TCGCAACGCGATTATGACTA
* * *
275892 TCGCAATGCGAATATGTA-AA
1 TCGCAACGCGATTATG-ACTA
*
275912 TCGCAACGCGATTCTGACTA
1 TCGCAACGCGATTATGACTA
275932 TCGCAACGCGAT
1 TCGCAACGCGAT
275944 AATACAAAAT
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
19 1 0.02
20 40 0.95
21 1 0.02
ACGTcount: A:0.29, C:0.25, G:0.21, T:0.25
Consensus pattern (20 bp):
TCGCAACGCGATTATGACTA
Found at i:276135 original size:22 final size:22
Alignment explanation
Indices: 276110--276160 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
276100 GTACAGCGAC
*
276110 ATCCGTCCCCATCTCCGACGAA
1 ATCCGTCCCCATCTCCGACAAA
* *
276132 ATCCATCCCCATCTCCGGCAAA
1 ATCCGTCCCCATCTCCGACAAA
276154 ATCCGTC
1 ATCCGTC
276161 TATCTGCATC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.24, C:0.45, G:0.12, T:0.20
Consensus pattern (22 bp):
ATCCGTCCCCATCTCCGACAAA
Found at i:276571 original size:19 final size:19
Alignment explanation
Indices: 276549--276592 Score: 72
Period size: 19 Copynumber: 2.3 Consensus size: 19
276539 AAATCGCAAC
276549 GCGATTTT-AGTTTCGCGTT
1 GCGATTTTCA-TTTCGCGTT
276568 GCGATTTTCATTTCGCGTT
1 GCGATTTTCATTTCGCGTT
276587 GCGATT
1 GCGATT
276593 ATCGATTGTC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 23 0.96
20 1 0.04
ACGTcount: A:0.11, C:0.18, G:0.25, T:0.45
Consensus pattern (19 bp):
GCGATTTTCATTTCGCGTT
Found at i:276623 original size:20 final size:20
Alignment explanation
Indices: 276595--276638 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
276585 TTGCGATTAT
*
276595 CGATTGTCAAATTCGCGTTG
1 CGATAGTCAAATTCGCGTTG
** *
276615 CGATAGTCATTTTCGTGTTG
1 CGATAGTCAAATTCGCGTTG
276635 CGAT
1 CGAT
276639 TTTAAGTTTC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.18, C:0.18, G:0.25, T:0.39
Consensus pattern (20 bp):
CGATAGTCAAATTCGCGTTG
Found at i:278680 original size:20 final size:20
Alignment explanation
Indices: 278643--278680 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
278633 AATCACAACG
**
278643 TGAAAATCGCAATGCGAAAA
1 TGAAAATCGCAACACGAAAA
278663 TGAAAATCGCAACACGAA
1 TGAAAATCGCAACACGAA
278681 TTTAGTTTCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.18, G:0.18, T:0.13
Consensus pattern (20 bp):
TGAAAATCGCAACACGAAAA
Found at i:278750 original size:20 final size:20
Alignment explanation
Indices: 278725--278772 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
278715 CGATTATCTT
*
278725 GTTGCGGTAGTCAAATTCGC
1 GTTGCGATAGTCAAATTCGC
**
278745 GTTGCGATAGTCATTTTCGC
1 GTTGCGATAGTCAAATTCGC
278765 GTTGCGAT
1 GTTGCGAT
278773 TTTAAGTTTC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.17, C:0.19, G:0.29, T:0.35
Consensus pattern (20 bp):
GTTGCGATAGTCAAATTCGC
Found at i:278782 original size:20 final size:20
Alignment explanation
Indices: 278740--278802 Score: 81
Period size: 20 Copynumber: 3.1 Consensus size: 20
278730 GGTAGTCAAA
** * *
278740 TTCGCGTTGCGATAGTCATT
1 TTCGCGTTGCGATTTTAAGT
278760 TTCGCGTTGCGATTTTAAGT
1 TTCGCGTTGCGATTTTAAGT
*
278780 TTCGTGTTGCGATTTTAAGT
1 TTCGCGTTGCGATTTTAAGT
278800 TTC
1 TTC
278803 AGAAACTATT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.14, C:0.16, G:0.24, T:0.46
Consensus pattern (20 bp):
TTCGCGTTGCGATTTTAAGT
Found at i:279367 original size:21 final size:21
Alignment explanation
Indices: 279276--279373 Score: 72
Period size: 21 Copynumber: 4.7 Consensus size: 21
279266 GACTCACATG
* *
279276 TCATCATTCAAGAGGCCTCTC
1 TCATCGTTCAAGAGGCCCCTC
*
279297 -CTATCGTTCAAGAGGCCCCTA
1 TC-ATCGTTCAAGAGGCCCCTC
* ** *
279318 TCACCCCTCAAGAGTCCCCTC
1 TCATCGTTCAAGAGGCCCCTC
* * * *
279339 CCACCGTTCAAGAGGCCCTTG
1 TCATCGTTCAAGAGGCCCCTC
*
279360 TCATCGTTGAAGAG
1 TCATCGTTCAAGAG
279374 TATCTCCCAC
Statistics
Matches: 58, Mismatches: 17, Indels: 4
0.73 0.22 0.05
Matches are distributed among these distances:
20 1 0.02
21 56 0.97
22 1 0.02
ACGTcount: A:0.22, C:0.36, G:0.18, T:0.23
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTC
Found at i:280946 original size:20 final size:20
Alignment explanation
Indices: 280921--280972 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
280911 AACGCTAAAC
*
280921 TCAAAATCTCAATACGAAAG
1 TCAAAATCGCAATACGAAAG
*
280941 TCAAAATCGCAATGCGAAAG
1 TCAAAATCGCAATACGAAAG
*
280961 CCAAAATCGCAA
1 TCAAAATCGCAA
280973 CGAGAAAGTC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.48, C:0.23, G:0.13, T:0.15
Consensus pattern (20 bp):
TCAAAATCGCAATACGAAAG
Found at i:280979 original size:20 final size:20
Alignment explanation
Indices: 280936--280980 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
280926 ATCTCAATAC
* * *
280936 GAAAGTCAAAATCGCAATGC
1 GAAAGCCAAAATCGCAACGA
280956 GAAAGCCAAAATCGCAACGA
1 GAAAGCCAAAATCGCAACGA
280976 GAAAG
1 GAAAG
280981 TCAATTCGCG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.49, C:0.20, G:0.22, T:0.09
Consensus pattern (20 bp):
GAAAGCCAAAATCGCAACGA
Found at i:281052 original size:20 final size:20
Alignment explanation
Indices: 281023--281159 Score: 202
Period size: 20 Copynumber: 6.8 Consensus size: 20
281013 GCGATTTTCT
*
281023 CGTTGCGATAGTCAAATTCC
1 CGTTGCGATAGTCAAATTCG
** * *
281043 CGTTATGATAATCAAATTCA
1 CGTTGCGATAGTCAAATTCG
*
281063 CGTTGTGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
281083 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
281103 CGTTGCGATAGTCAAATTTG
1 CGTTGCGATAGTCAAATTCG
281123 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
281143 CGTTGCGATATTCAAAT
1 CGTTGCGATAGTCAAAT
281160 GAATGTGTAA
Statistics
Matches: 106, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 106 1.00
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.33
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:281078 original size:40 final size:40
Alignment explanation
Indices: 280979--281159 Score: 205
Period size: 40 Copynumber: 4.7 Consensus size: 40
280969 GCAACGAGAA
* * *
280979 AGTC-AATTCGCGTTGCGATAGTCTAATACGCTTTGCGAT
1 AGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGAT
* * **
281018 --T----TTCTCGTTGCGATAGTCAAATTCCCGTTATGAT
1 AGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGAT
* * *
281052 AATCAAATTCACGTTGTGATAGTCAAATTCGCGTTGCGAT
1 AGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGAT
*
281092 AGTCAAATTCGCGTTGCGATAGTCAAATTTGCGTTGCGAT
1 AGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGAT
*
281132 AGTCAAATTCGCGTTGCGATATTCAAAT
1 AGTCAAATTCGCGTTGCGATAGTCAAAT
281160 GAATGTGTAA
Statistics
Matches: 119, Mismatches: 17, Indels: 11
0.81 0.12 0.07
Matches are distributed among these distances:
34 26 0.22
36 1 0.01
37 1 0.01
40 91 0.76
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (40 bp):
AGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGAT
Found at i:281351 original size:12 final size:12
Alignment explanation
Indices: 281327--281364 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
281317 GTGAAGCCCG
*
281327 TTGTGA-TTGGA
1 TTGTGATTTTGA
*
281338 TTTTGATTTTGA
1 TTGTGATTTTGA
281350 TTGTGATTTTGA
1 TTGTGATTTTGA
281362 TTG
1 TTG
281365 CCTTTTGCTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
11 5 0.22
12 18 0.78
ACGTcount: A:0.16, C:0.00, G:0.26, T:0.58
Consensus pattern (12 bp):
TTGTGATTTTGA
Found at i:281359 original size:18 final size:17
Alignment explanation
Indices: 281330--281363 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
281320 AAGCCCGTTG
281330 TGATTGGATTTTGATTT
1 TGATTGGATTTTGATTT
281347 TGATTGTGATTTTGATT
1 TGATTG-GATTTTGATT
281364 GCCTTTTGCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.18, C:0.00, G:0.24, T:0.59
Consensus pattern (17 bp):
TGATTGGATTTTGATTT
Found at i:284305 original size:17 final size:18
Alignment explanation
Indices: 284279--284316 Score: 69
Period size: 17 Copynumber: 2.2 Consensus size: 18
284269 TGTCGGATGG
284279 GGATGATTGTTGGATATA
1 GGATGATTGTTGGATATA
284297 GGATG-TTGTTGGATATA
1 GGATGATTGTTGGATATA
284314 GGA
1 GGA
284317 ACGGATGTCG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 15 0.75
18 5 0.25
ACGTcount: A:0.26, C:0.00, G:0.37, T:0.37
Consensus pattern (18 bp):
GGATGATTGTTGGATATA
Found at i:284488 original size:20 final size:20
Alignment explanation
Indices: 284463--284530 Score: 66
Period size: 20 Copynumber: 3.4 Consensus size: 20
284453 GAAATTCAGT
* *
284463 GTTGCGATAGTCAGAATCAC
1 GTTGCGATAGTCAAAATCGC
* **
284483 GTTGCGATTTTGT-ATTATCGC
1 GTTGCGA--TAGTCAAAATCGC
284504 GTTGCGATAGTCAAAATCGC
1 GTTGCGATAGTCAAAATCGC
284524 GTTGCGA
1 GTTGCGA
284531 ATCTGGAAAC
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
19 3 0.08
20 20 0.53
21 12 0.32
22 3 0.08
ACGTcount: A:0.24, C:0.18, G:0.26, T:0.32
Consensus pattern (20 bp):
GTTGCGATAGTCAAAATCGC
Found at i:284491 original size:41 final size:41
Alignment explanation
Indices: 284442--284530 Score: 117
Period size: 41 Copynumber: 2.2 Consensus size: 41
284432 ACTAAAACCT
* *
284442 GTTGCGATTTTGAAAT-TCAGTGTTGCGATAGTCAGAATCAC
1 GTTGCGATTTTGAAATATC-GCGTTGCGATAGTCAAAATCAC
* * *
284483 GTTGCGATTTTGTATTATCGCGTTGCGATAGTCAAAATCGC
1 GTTGCGATTTTGAAATATCGCGTTGCGATAGTCAAAATCAC
284524 GTTGCGA
1 GTTGCGA
284531 ATCTGGAAAC
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
41 40 0.95
42 2 0.05
ACGTcount: A:0.24, C:0.16, G:0.26, T:0.35
Consensus pattern (41 bp):
GTTGCGATTTTGAAATATCGCGTTGCGATAGTCAAAATCAC
Found at i:284568 original size:20 final size:19
Alignment explanation
Indices: 284545--284590 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
284535 GGAAACTGAT
* *
284545 TTGCGATACTGGAGATCGCG
1 TTGCGAT-CTAGAGATCGCA
*
284565 TTGCGATTTAGAGATCGCA
1 TTGCGATCTAGAGATCGCA
284584 TTGCGAT
1 TTGCGAT
284591 TTTGTTGGTC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.22, C:0.17, G:0.30, T:0.30
Consensus pattern (19 bp):
TTGCGATCTAGAGATCGCA
Found at i:284580 original size:19 final size:19
Alignment explanation
Indices: 284556--284592 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
284546 TGCGATACTG
*
284556 GAGATCGCGTTGCGATTTA
1 GAGATCGCATTGCGATTTA
284575 GAGATCGCATTGCGATTT
1 GAGATCGCATTGCGATTT
284593 TGTTGGTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.22, C:0.16, G:0.30, T:0.32
Consensus pattern (19 bp):
GAGATCGCATTGCGATTTA
Found at i:284894 original size:21 final size:22
Alignment explanation
Indices: 284855--284895 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
284845 TGTGATGGTT
284855 TTTAACATAAAATATTATATTA
1 TTTAACATAAAATATTATATTA
*
284877 TTTAACCTAAAA-ATTATAT
1 TTTAACATAAAATATTATAT
284896 AAATTTATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (22 bp):
TTTAACATAAAATATTATATTA
Found at i:284901 original size:22 final size:22
Alignment explanation
Indices: 284855--284902 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
284845 TGTGATGGTT
*
284855 TTTAACATAAAATATTATATTA
1 TTTAACATAAAATATTATATAA
*
284877 TTTAACCTAAAA-ATTATATAAA
1 TTTAACATAAAATATTATAT-AA
284899 TTTA
1 TTTA
284903 TAATATTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 7 0.30
22 16 0.70
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (22 bp):
TTTAACATAAAATATTATATAA
Found at i:287898 original size:45 final size:45
Alignment explanation
Indices: 287834--287971 Score: 164
Period size: 45 Copynumber: 3.2 Consensus size: 45
287824 TAATCCAAGA
287834 CTTTTGATTATTAGGTTGTCAAAAGTAAAATCAAAGGATTAGTTC
1 CTTTTGATTATTAGGTTGTCAAAAGTAAAATCAAAGGATTAGTTC
*
287879 CTTTTGATTATT-GTGTTGTCAAAAGTAAAATCAAATGATTAGTTC
1 CTTTTGATTATTAG-GTTGTCAAAAGTAAAATCAAAGGATTAGTTC
* * * * *
287924 ATTTTTATTATTTGGTTG------GTAAAATTAAAGGATTAATTC
1 CTTTTGATTATTAGGTTGTCAAAAGTAAAATCAAAGGATTAGTTC
287963 CTTTTGATT
1 CTTTTGATT
287972 TCTGTTTGTT
Statistics
Matches: 83, Mismatches: 8, Indels: 10
0.82 0.08 0.10
Matches are distributed among these distances:
39 25 0.30
44 1 0.01
45 56 0.67
46 1 0.01
ACGTcount: A:0.33, C:0.07, G:0.16, T:0.44
Consensus pattern (45 bp):
CTTTTGATTATTAGGTTGTCAAAAGTAAAATCAAAGGATTAGTTC
Found at i:288180 original size:58 final size:58
Alignment explanation
Indices: 288087--288501 Score: 450
Period size: 58 Copynumber: 7.1 Consensus size: 58
288077 TTTCATCGTT
* * * * * *
288087 AGAATCTTGAATTGATTTTAACTTTGTAAGAAAAATAGATTGTTGAATTTATTTCCTTG
1 AGAATCTT-AAATGATTTTATCTTTGTAAGGAAAATAAATTGTTAAATTTATTTTCTTG
* * * *
288146 AGAGTCTTAAATGATTCTATCTTTGTAAGGAAAATAAATTGTTGAATTTATTTCCTTG
1 AGAATCTTAAATGATTTTATCTTTGTAAGGAAAATAAATTGTTAAATTTATTTTCTTG
* * * * *
288204 AAAATCTTGAATGATTTTAACTTTGTAAGAAAAATAAATTGTCAAATTTATTTTCTTG
1 AGAATCTTAAATGATTTTATCTTTGTAAGGAAAATAAATTGTTAAATTTATTTTCTTG
* ** ** *
288262 AGAATCGTGGATGATTTTACTCTTTAAAAAG-AAATAAATTGTTAAATTTATTTTCTTG
1 AGAATCTTAAATGATTTTA-TCTTTGTAAGGAAAATAAATTGTTAAATTTATTTTCTTG
* * * *
288320 AGAATCTTAAATTATTCTT-T-TTTGTAA-AAATTAATAAATTGTTAAATTTATTTTATTA
1 AGAATCTTAAATGATT-TTATCTTTGTAAGGAA--AATAAATTGTTAAATTTATTTTCTTG
*
288378 AGAATCTTAAATGATTTTAT-TTTGTTAAAGG-AAATAAATTGTTAAATTTATTTTATTG
1 AGAATCTTAAATGATTTTATCTTTG-T-AAGGAAAATAAATTGTTAAATTTATTTTCTTG
*
288436 AGAATCTTAAATGATTCTAT-TTTGTTAATGG-AAATAAATTGTTAAATTTATTTTCTTG
1 AGAATCTTAAATGATTTTATCTTTG-TAA-GGAAAATAAATTGTTAAATTTATTTTCTTG
288494 AGAATCTT
1 AGAATCTT
288502 GAATAAATAA
Statistics
Matches: 308, Mismatches: 38, Indels: 21
0.84 0.10 0.06
Matches are distributed among these distances:
56 6 0.02
57 5 0.02
58 278 0.90
59 16 0.05
60 3 0.01
ACGTcount: A:0.36, C:0.06, G:0.12, T:0.46
Consensus pattern (58 bp):
AGAATCTTAAATGATTTTATCTTTGTAAGGAAAATAAATTGTTAAATTTATTTTCTTG
Found at i:288397 original size:27 final size:27
Alignment explanation
Indices: 288366--288463 Score: 74
Period size: 27 Copynumber: 3.5 Consensus size: 27
288356 AATTGTTAAA
288366 TTTATTTTATTAAGAATCTTAAATGAT
1 TTTATTTTATTAAGAATCTTAAATGAT
* * *
288393 TTTATTTTGTTAAAGGAA--ATAAATTGTTAAA
1 TTTATTTTATT-AA-GAATCTTAAA-TG---AT
*
288424 TTTATTTTATTGAGAATCTTAAATGAT
1 TTTATTTTATTAAGAATCTTAAATGAT
* *
288451 TCTATTTTGTTAA
1 TTTATTTTATTAA
288464 TGGAAATAAA
Statistics
Matches: 53, Mismatches: 10, Indels: 16
0.67 0.13 0.20
Matches are distributed among these distances:
27 25 0.47
28 4 0.08
29 6 0.11
30 3 0.06
31 15 0.28
ACGTcount: A:0.36, C:0.03, G:0.10, T:0.51
Consensus pattern (27 bp):
TTTATTTTATTAAGAATCTTAAATGAT
Found at i:288473 original size:27 final size:27
Alignment explanation
Indices: 288385--288474 Score: 65
Period size: 27 Copynumber: 3.2 Consensus size: 27
288375 TTAAGAATCT
* *
288385 TAAATGATTTTATTTTGTTAAAGGAAA
1 TAAATGATTATATTTTGTTAATGGAAA
* * * *
288412 TAAATTG-TTAAATTTATTTTATTGAGAATCT
1 TAAA-TGATTATATTT-TGTTAATG-GAA--A
*
288443 TAAATGATTCTATTTTGTTAATGGAAA
1 TAAATGATTATATTTTGTTAATGGAAA
288470 TAAAT
1 TAAAT
288475 TGTTAAATTT
Statistics
Matches: 46, Mismatches: 11, Indels: 12
0.67 0.16 0.17
Matches are distributed among these distances:
27 15 0.33
28 7 0.15
29 6 0.13
30 8 0.17
31 10 0.22
ACGTcount: A:0.39, C:0.02, G:0.12, T:0.47
Consensus pattern (27 bp):
TAAATGATTATATTTTGTTAATGGAAA
Found at i:288484 original size:27 final size:27
Alignment explanation
Indices: 288396--288484 Score: 72
Period size: 27 Copynumber: 3.1 Consensus size: 27
288386 AAATGATTTT
*
288396 ATTTTGTTAAAGGAAATAAATTGTTAA
1 ATTTTGTTAATGGAAATAAATTGTTAA
* * * **
288423 ATTTATTTTATTGAGAATCTTAAA-TGATTCT
1 ATTT-TGTTAATG-GAA--ATAAATTG-TTAA
288454 ATTTTGTTAATGGAAATAAATTGTTAA
1 ATTTTGTTAATGGAAATAAATTGTTAA
288481 ATTT
1 ATTT
288485 ATTTTCTTGA
Statistics
Matches: 45, Mismatches: 11, Indels: 12
0.66 0.16 0.18
Matches are distributed among these distances:
27 14 0.31
28 7 0.16
29 6 0.13
30 8 0.18
31 10 0.22
ACGTcount: A:0.38, C:0.02, G:0.12, T:0.47
Consensus pattern (27 bp):
ATTTTGTTAATGGAAATAAATTGTTAA
Found at i:288630 original size:38 final size:37
Alignment explanation
Indices: 288544--288653 Score: 111
Period size: 38 Copynumber: 3.0 Consensus size: 37
288534 ATATGATTCA
* *
288544 ATTTTAAAAGGGAATAAATTGTTGGATTT-TTTT--T
1 ATTTTAAAAGGAAATAAATTGTTGAATTTATTTTCCT
**
288578 -TTTGTAAATTGAAATAAATTGTTGAATTTATTTTCCT
1 ATTT-TAAAAGGAAATAAATTGTTGAATTTATTTTCCT
* * *
288615 ATTTTAAAAAGGAAATAAATCGGTAAATTTATTTTCCT
1 ATTTT-AAAAGGAAATAAATTGTTGAATTTATTTTCCT
288653 A
1 A
288654 AGAATTTTGT
Statistics
Matches: 61, Mismatches: 9, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
33 3 0.05
34 21 0.34
35 4 0.07
37 2 0.03
38 31 0.51
ACGTcount: A:0.36, C:0.05, G:0.13, T:0.46
Consensus pattern (37 bp):
ATTTTAAAAGGAAATAAATTGTTGAATTTATTTTCCT
Found at i:288728 original size:39 final size:39
Alignment explanation
Indices: 288679--288850 Score: 175
Period size: 39 Copynumber: 4.4 Consensus size: 39
288669 TCTGATATGT
* * *
288679 AAAAGAAAATAAATCATTGAATTTATTTTCCTATTTTAA
1 AAAAGGAAATAAATCATTGAATTTAGTTTCCTATTTTTA
* * * *
288718 AAAAGGAAATAAACCATAGAATTTAGTTTCCTGGTTTGT-
1 AAAAGGAAATAAATCATTGAATTTAGTTTCCT-ATTTTTA
* * *
288757 AAAAGGAAATAAATCATTGGATTTATTTTCTTATTTTGTA
1 AAAAGGAAATAAATCATTGAATTTAGTTTCCTATTTT-TA
* * * * * *
288797 AAAAGGAAATAAACCGTTGGATTTAGTTTACTGTTTTTT
1 AAAAGGAAATAAATCATTGAATTTAGTTTCCTATTTTTA
288836 AAAAGGAAATAAATC
1 AAAAGGAAATAAATC
288851 GAAAAAAATC
Statistics
Matches: 108, Mismatches: 22, Indels: 6
0.79 0.16 0.04
Matches are distributed among these distances:
38 3 0.03
39 71 0.66
40 34 0.31
ACGTcount: A:0.41, C:0.08, G:0.13, T:0.38
Consensus pattern (39 bp):
AAAAGGAAATAAATCATTGAATTTAGTTTCCTATTTTTA
Found at i:288875 original size:167 final size:167
Alignment explanation
Indices: 288683--288987 Score: 409
Period size: 167 Copynumber: 1.8 Consensus size: 167
288673 ATATGTAAAA
288683 GAAAATAAATCATTGAATTTATTTTCCTATTTTAAAAAAGGAAATAAA-CCATAGAATTTAGTTT
1 GAAAATAAATCATTGAATTTATTTTCCTATTTTAAAAAAGGAAATAAATCCATAG-ATTTAGTTT
* *
288747 CCTGGTTTGTAAAAGGAAATAAATCATTGGATTTATTTTCTTATTTTGTAAAAAGGAAATAAACC
65 CCTGGTTTGTAAAAGAAAATAAATCATTGGATTTATTTTCATATTTTGT-AAAAGGAAATAAACC
*
288812 GTTGGATTTAGTTTACTGTTTTTTAAAAGGAAATAAATC
129 ATTGGATTTAGTTTACTGTTTTTTAAAAGGAAATAAATC
* * ** ** * *
288851 GAAAA-AAATCATTTG-ATTTATTTTCTTGTTTTGTAAAAGGAAATAAATCGTTTGATTTATTTT
1 GAAAATAAATCA-TTGAATTTATTTTCCTATTTTAAAAAAGGAAATAAATCCATAGATTTAGTTT
* * * * * *
288914 TCTGTTTTGTGAAAGAAAATAAATCGTTGGATTTATTTTCATGTTTTGTAAAAGGAAATAAATCA
65 CCTGGTTTGTAAAAGAAAATAAATCATTGGATTTATTTTCATATTTTGTAAAAGGAAATAAACCA
288979 TTGGATTTA
130 TTGGATTTA
288988 TTTTTTTGGG
Statistics
Matches: 118, Mismatches: 17, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
166 23 0.19
167 84 0.71
168 11 0.09
ACGTcount: A:0.38, C:0.07, G:0.14, T:0.41
Consensus pattern (167 bp):
GAAAATAAATCATTGAATTTATTTTCCTATTTTAAAAAAGGAAATAAATCCATAGATTTAGTTTC
CTGGTTTGTAAAAGAAAATAAATCATTGGATTTATTTTCATATTTTGTAAAAGGAAATAAACCAT
TGGATTTAGTTTACTGTTTTTTAAAAGGAAATAAATC
Found at i:288910 original size:39 final size:39
Alignment explanation
Indices: 288851--288991 Score: 194
Period size: 39 Copynumber: 3.6 Consensus size: 39
288841 GAAATAAATC
* *
288851 GAAAAAAATCATTTGATTTATTTTCTTGTTTTGTAAAAG
1 GAAATAAATCATTGGATTTATTTTCTTGTTTTGTAAAAG
* * *
288890 GAAATAAATCGTTTGATTTATTTT-TCTGTTTTGTGAAAG
1 GAAATAAATCATTGGATTTATTTTCT-TGTTTTGTAAAAG
* * *
288929 AAAATAAATCGTTGGATTTATTTTCATGTTTTGTAAAAG
1 GAAATAAATCATTGGATTTATTTTCTTGTTTTGTAAAAG
288968 GAAATAAATCATTGGATTTATTTT
1 GAAATAAATCATTGGATTTATTTT
288992 TTTGGGAATC
Statistics
Matches: 91, Mismatches: 9, Indels: 4
0.88 0.09 0.04
Matches are distributed among these distances:
38 1 0.01
39 90 0.99
ACGTcount: A:0.34, C:0.05, G:0.15, T:0.46
Consensus pattern (39 bp):
GAAATAAATCATTGGATTTATTTTCTTGTTTTGTAAAAG
Found at i:288934 original size:88 final size:87
Alignment explanation
Indices: 288762--288992 Score: 273
Period size: 78 Copynumber: 2.7 Consensus size: 87
288752 TTTGTAAAAG
* * * *
288762 GAAATAAATCATTGGATTTATTTTCTTATTTTGTAAAAAGGAAATAAACCGTTGGATTTAGTTTA
1 GAAA-AAATCATTGGATTTATTTTCTTGTTTTGT-AAAAGGAAATAAATCGTTGGATTTATTTTT
* *
288827 CTGTTTTTTAAAAGGAAATAAATC
64 CTGTTTTGTAAAAGAAAATAAATC
* *
288851 GAAAAAAATCATTTGATTTATTTTCTTGTTTTGTAAAAGGAAATAAATCGTTTGATTTATTTTTC
1 G-AAAAAATCATTGGATTTATTTTCTTGTTTTGTAAAAGGAAATAAATCGTTGGATTTATTTTTC
*
288916 TGTTTTGTGAAAGAAAATAAATC
65 TGTTTTGTAAAAGAAAATAAATC
* *
288939 G---------TTGGATTTATTTTCATGTTTTGTAAAAGGAAATAAATCATTGGATTTATTTTT
1 GAAAAAATCATTGGATTTATTTTCTTGTTTTGTAAAAGGAAATAAATCGTTGGATTTATTTTT
288993 TTGGGAATCT
Statistics
Matches: 128, Mismatches: 13, Indels: 13
0.83 0.08 0.08
Matches are distributed among these distances:
78 49 0.38
88 48 0.38
89 28 0.22
90 3 0.02
ACGTcount: A:0.35, C:0.06, G:0.15, T:0.44
Consensus pattern (87 bp):
GAAAAAATCATTGGATTTATTTTCTTGTTTTGTAAAAGGAAATAAATCGTTGGATTTATTTTTCT
GTTTTGTAAAAGAAAATAAATC
Found at i:295075 original size:18 final size:18
Alignment explanation
Indices: 295054--295101 Score: 89
Period size: 18 Copynumber: 2.7 Consensus size: 18
295044 TGAGGTGGAT
295054 GAAGAAGATGATGAACAA
1 GAAGAAGATGATGAACAA
295072 GAAGAAGATGATGAACAA
1 GAAGAAGATGATGAACAA
295090 GAAGAAGA-GATG
1 GAAGAAGATGATG
295102 GTCAAGCTCT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
17 4 0.13
18 26 0.87
ACGTcount: A:0.54, C:0.04, G:0.31, T:0.10
Consensus pattern (18 bp):
GAAGAAGATGATGAACAA
Found at i:296687 original size:21 final size:21
Alignment explanation
Indices: 296648--296686 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
296638 AAACAATTAG
296648 TAACAATTGATATTATTTTGT
1 TAACAATTGATATTATTTTGT
*
296669 TAACAATTGGTA-TATTTT
1 TAACAATTGATATTATTTT
296687 TCATTAAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.33, C:0.05, G:0.10, T:0.51
Consensus pattern (21 bp):
TAACAATTGATATTATTTTGT
Found at i:296958 original size:23 final size:21
Alignment explanation
Indices: 296907--296966 Score: 68
Period size: 23 Copynumber: 2.8 Consensus size: 21
296897 AGGGTGTCAA
*
296907 AGTGCATCCATGCACCCCTGC
1 AGTGCATCCATGCACCCCTAC
296928 AGTGCATCCATGCACCTGCC-AC
1 AGTGCATCCATGCACC--CCTAC
*
296950 TAGTGCATCGATGCACC
1 -AGTGCATCCATGCACC
296967 ATGTTATGGG
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
21 16 0.47
22 1 0.03
23 17 0.50
ACGTcount: A:0.22, C:0.38, G:0.20, T:0.20
Consensus pattern (21 bp):
AGTGCATCCATGCACCCCTAC
Found at i:304739 original size:24 final size:23
Alignment explanation
Indices: 304712--304758 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
304702 CAATTTAATA
304712 GTTATAATTTATATTTAATTTCTT
1 GTTATAATTTATATTT-ATTTCTT
* *
304736 GTTATCATTTTTATTTATTTCTT
1 GTTATAATTTATATTTATTTCTT
304759 ATATAAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 7 0.33
24 14 0.67
ACGTcount: A:0.23, C:0.06, G:0.04, T:0.66
Consensus pattern (23 bp):
GTTATAATTTATATTTATTTCTT
Found at i:312366 original size:18 final size:19
Alignment explanation
Indices: 312343--312379 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
312333 AATTGTCCCT
312343 TGTTTTTA-TCGTAATAGG
1 TGTTTTTATTCGTAATAGG
312361 TGTTTTTATTCGTAATAGG
1 TGTTTTTATTCGTAATAGG
312380 GTAATGAGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.22, C:0.05, G:0.22, T:0.51
Consensus pattern (19 bp):
TGTTTTTATTCGTAATAGG
Found at i:313128 original size:23 final size:23
Alignment explanation
Indices: 313102--313150 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
313092 TTTAAAATCG
*
313102 AAAACCAAATTAAATTAACT-AAT
1 AAAACCAAA-TAAACTAACTGAAT
*
313125 AAAATCAAATAAACTAACTGAAT
1 AAAACCAAATAAACTAACTGAAT
313148 AAA
1 AAA
313151 TAAAAAGCAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 9 0.39
23 14 0.61
ACGTcount: A:0.63, C:0.12, G:0.02, T:0.22
Consensus pattern (23 bp):
AAAACCAAATAAACTAACTGAAT
Found at i:314651 original size:14 final size:15
Alignment explanation
Indices: 314632--314661 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
314622 AATTAAAATA
314632 AAATTGCA-AAATTT
1 AAATTGCAGAAATTT
314646 AAATTGCAGAAATTT
1 AAATTGCAGAAATTT
314661 A
1 A
314662 GATTACTGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.50, C:0.07, G:0.10, T:0.33
Consensus pattern (15 bp):
AAATTGCAGAAATTT
Found at i:320233 original size:9 final size:9
Alignment explanation
Indices: 320221--320245 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
320211 TATTCATTTT
320221 AATTAAAAA
1 AATTAAAAA
320230 AATTAAAAA
1 AATTAAAAA
320239 AATTAAA
1 AATTAAA
320246 GTATATTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (9 bp):
AATTAAAAA
Found at i:322477 original size:20 final size:21
Alignment explanation
Indices: 322452--322510 Score: 75
Period size: 22 Copynumber: 2.8 Consensus size: 21
322442 CTTGGAGCGT
322452 GGGGGGAATCGGTACCCCCAGG
1 GGGGGGAATCGGTACCCCCA-G
* * *
322474 GGGGGGAATCTGTTCCCCC-T
1 GGGGGGAATCGGTACCCCCAG
322494 GGGGGGAATCGGTACCC
1 GGGGGGAATCGGTACCC
322511 ATTTGGGGGG
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
20 15 0.47
22 17 0.53
ACGTcount: A:0.15, C:0.27, G:0.42, T:0.15
Consensus pattern (21 bp):
GGGGGGAATCGGTACCCCCAG
Found at i:322510 original size:42 final size:42
Alignment explanation
Indices: 322451--322537 Score: 122
Period size: 42 Copynumber: 2.1 Consensus size: 42
322441 GCTTGGAGCG
*
322451 TGGGGGGAATCGGTACCC-CCAGGGGGGGGAATCTGTTCCCCC
1 TGGGGGGAATCGGTACCCACCAGGGGGGGG-ATCTGTACCCCC
***
322493 TGGGGGGAATCGGTACCCATTTGGGGGGGGATCTGTACCCCC
1 TGGGGGGAATCGGTACCCACCAGGGGGGGGATCTGTACCCCC
322535 TGG
1 TGG
322538 ACATTCTGTT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
42 32 0.80
43 8 0.20
ACGTcount: A:0.14, C:0.25, G:0.41, T:0.20
Consensus pattern (42 bp):
TGGGGGGAATCGGTACCCACCAGGGGGGGGATCTGTACCCCC
Found at i:322920 original size:20 final size:21
Alignment explanation
Indices: 322895--322933 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
322885 TGTTGTATCT
322895 AGCCGTTGGGGATG-TTTTGG
1 AGCCGTTGGGGATGATTTTGG
*
322915 AGCCGTTTGGGATGATTTT
1 AGCCGTTGGGGATGATTTT
322934 TCTGCAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.13, C:0.10, G:0.38, T:0.38
Consensus pattern (21 bp):
AGCCGTTGGGGATGATTTTGG
Found at i:323056 original size:20 final size:20
Alignment explanation
Indices: 323031--323090 Score: 102
Period size: 20 Copynumber: 3.0 Consensus size: 20
323021 CCGTTGCAGC
323031 CAGGGTGCATGGATGCACTG
1 CAGGGTGCATGGATGCACTG
*
323051 CAGGGTGCATGGATGCACTA
1 CAGGGTGCATGGATGCACTG
*
323071 CAAGGTGCATGGATGCACTG
1 CAGGGTGCATGGATGCACTG
323091 TGCATCGGTA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.23, C:0.20, G:0.37, T:0.20
Consensus pattern (20 bp):
CAGGGTGCATGGATGCACTG
Found at i:323216 original size:20 final size:20
Alignment explanation
Indices: 323193--323243 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
323183 TGCACAATGT
323193 ATGGATACACTGCAGAGTGC
1 ATGGATACACTGCAGAGTGC
* * *
323213 ATGGATATACTGCAGGGTGT
1 ATGGATACACTGCAGAGTGC
323233 ATGGATACACT
1 ATGGATACACT
323244 TTGACACCCT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.25
Consensus pattern (20 bp):
ATGGATACACTGCAGAGTGC
Done.